@article {958, title = {Autosomal recessive variants in alter the γ-tubulin ring complex leading to neurodevelopmental disease.}, journal = {iScience}, volume = {24}, year = {2021}, month = {2021 Jan 22}, pages = {101948}, abstract = {

Microtubules help building the cytoskeleton of neurons and other cells. Several components of the gamma-tubulin (γ-tubulin) complex have been previously reported in human neurodevelopmental diseases. We describe two siblings from a consanguineous Turkish family with dysmorphic features, developmental delay, brain malformation, and epilepsy carrying a homozygous mutation (p.Glu311Lys) in encoding the γ-tubulin complex 2 (GCP2) protein. This variant is predicted to disrupt the electrostatic interaction of GCP2 with GCP3. In primary fibroblasts carrying the variant, we observed a faint delocalization of γ-tubulin during the cell cycle but normal GCP2 protein levels. Through mass spectrometry, we observed dysregulation of multiple proteins involved in the assembly and organization of the cytoskeleton and the extracellular matrix, controlling cellular adhesion and of proteins crucial for neuronal homeostasis including axon guidance. In summary, our functional and proteomic studies link TUBGCP2 and the γ-tubulin complex to the development of the central nervous system in humans.

}, issn = {2589-0042}, doi = {10.1016/j.isci.2020.101948}, author = {G{\"u}ng{\"o}r, Serdal and Oktay, Yavuz and Hiz, Semra and Aranguren-Ib{\'a}{\~n}ez, {\'A}lvaro and Kalafatcilar, Ipek and Yaramis, Ahmet and Karaca, Ezgi and Yis, Uluc and Sonmezler, Ece and Ekinci, Burcu and Aslan, Mahmut and Yilmaz, Elmasnur and {\"O}zg{\"o}r, Bilge and Balaraju, Sunitha and Szabo, Nora and Laurie, Steven and Beltran, Sergi and MacArthur, Daniel G and Hathazi, Denisa and Topf, Ana and Roos, Andreas and Lochm{\"u}ller, Hanns and Vernos, Isabelle and Horvath, Rita} } @article {1013, title = {Novel variants in TUBA1A cause congenital fibrosis of the extraocular muscles with or without malformations of cortical brain development.}, journal = {Eur J Hum Genet}, volume = {29}, year = {2021}, month = {2021 May}, pages = {816-826}, abstract = {

Variants in multiple tubulin genes have been implicated in neurodevelopmental disorders, including malformations of cortical development (MCD) and congenital fibrosis of the extraocular muscles (CFEOM). Distinct missense variants in the beta-tubulin encoding genes TUBB3 and TUBB2B cause MCD, CFEOM, or both, suggesting substitution-specific mechanisms. Variants in the alpha tubulin-encoding gene TUBA1A have been associated with MCD, but not with CFEOM. Using exome sequencing (ES) and genome sequencing (GS), we identified 3 unrelated probands with CFEOM who harbored novel heterozygous TUBA1A missense variants c.1216C>G, p.(His406Asp); c.467G>A, p.(Arg156His); and c.1193T>G, p.(Met398Arg). MRI revealed small oculomotor-innervated muscles and asymmetrical caudate heads and lateral ventricles with or without corpus callosal thinning. Two of the three probands had MCD. Mutated amino acid residues localize either to the longitudinal interface at which α and β tubulins heterodimerize (Met398, His406) or to the lateral interface at which tubulin protofilaments interact (Arg156), and His406 interacts with the motor domain of kinesin-1. This series of individuals supports TUBA1A variants as a cause of CFEOM and expands our knowledge of tubulinopathies.

}, issn = {1476-5438}, doi = {10.1038/s41431-020-00804-7}, author = {Jurgens, Julie A and Barry, Brenda J and Lemire, Gabrielle and Chan, Wai-Man and Whitman, Mary C and Shaaban, Sherin and Robson, Caroline D and MacKinnon, Sarah and England, Eleina M and McMillan, Hugh J and Kelly, Christopher and Pratt, Brandon M and O{\textquoteright}Donnell-Luria, Anne and MacArthur, Daniel G and Boycott, Kym M and Hunter, David G and Engle, Elizabeth C} } @article {971, title = {Pathogenic deep intronic MTM1 variant activates a pseudo-exon encoding a nonsense codon resulting in severe X-linked myotubular myopathy.}, journal = {Eur J Hum Genet}, volume = {29}, year = {2021}, month = {2021 Jan}, pages = {61-66}, abstract = {

X-linked myotubular myopathy (XLMTM) is a severe congenital myopathy characterised by generalised weakness and respiratory insufficiency. XLMTM is associated with pathogenic variants in MTM1; a gene encoding the lipid phosphatase myotubularin. Whole genome sequencing (WGS) of an exome-negative male proband with severe hypotonia, respiratory insufficiency and centralised nuclei on muscle biopsy identified a deep intronic MTM1 variant NG_008199.1(NM_000252.2):c.1468-577A>G, which strengthened a cryptic 5{\textquoteright} splice site (A>G substitution at the +5 position). Muscle RNA sequencing was non-diagnostic due to low read depth. Reverse transcription PCR (RT-PCR) of muscle RNA confirmed the c.1468-577A>G variant activates inclusion of a pseudo-exon encoding a premature stop codon into all detected MTM1 transcripts. Western blot analysis establishes deficiency of myotubularin protein, consistent with the severe XLMTM phenotype. We expand the genotypic spectrum of XLMTM and highlight benefits of screening non-coding regions of MTM1 in male probands with phenotypically concordant XLMTM who remain undiagnosed following exome sequencing.

}, issn = {1476-5438}, doi = {10.1038/s41431-020-00715-7}, author = {Bryen, Samantha J and Oates, Emily C and Evesson, Frances J and Lu, Jessica K and Waddell, Leigh B and Joshi, Himanshu and Ryan, Monique M and Cummings, Beryl B and McLean, Catriona A and MacArthur, Daniel G and Kornberg, Andrew J and Cooper, Sandra T} } @article {974, title = {Variants in GNAI1 cause a syndrome associated with variable features including developmental delay, seizures, and hypotonia.}, journal = {Genet Med}, volume = {23}, year = {2021}, month = {2021 05}, pages = {881-887}, abstract = {

PURPOSE: Neurodevelopmental disorders (NDDs) encompass a spectrum of genetically heterogeneous disorders with features that commonly include developmental delay, intellectual disability, and autism spectrum disorders. We sought to delineate the molecular and phenotypic spectrum of a novel neurodevelopmental disorder caused by variants in the GNAI1 gene.

METHODS: Through large cohort trio-based exome sequencing and international data-sharing, we identified 24 unrelated individuals with NDD phenotypes and a variant in GNAI1, which encodes the inhibitory Gαi1 subunit of heterotrimeric G-proteins. We collected detailed genotype and phenotype information for each affected individual.

RESULTS: We identified 16 unique variants in GNAI1 in 24 affected individuals; 23 occurred de novo and 1 was inherited from a mosaic parent. Most affected individuals have a severe neurodevelopmental disorder. Core features include global developmental delay, intellectual disability, hypotonia, and epilepsy.

CONCLUSION: This collaboration establishes GNAI1 variants as a cause of NDDs. GNAI1-related NDD is most often characterized by severe to profound delays, hypotonia, epilepsy that ranges from self-limiting to intractable, behavior problems, and variable mild dysmorphic features.

}, keywords = {Child, Developmental Disabilities, Humans, Intellectual Disability, Muscle Hypotonia, Neurodevelopmental Disorders, Seizures, Whole Exome Sequencing}, issn = {1530-0366}, doi = {10.1038/s41436-020-01076-8}, author = {Muir, Alison M and Gardner, Jennifer F and van Jaarsveld, Richard H and de Lange, Iris M and van der Smagt, Jasper J and Wilson, Golder N and Dubbs, Holly and Goldberg, Ethan M and Zitano, Lia and Bupp, Caleb and Martinez, Jose and Srour, Myriam and Accogli, Andrea and Alhakeem, Afnan and Meltzer, Meira and Gropman, Andrea and Brewer, Carole and Caswell, Richard C and Montgomery, Tara and McKenna, Caoimhe and McKee, Shane and Powell, Corinna and Vasudevan, Pradeep C and Brady, Angela F and Joss, Shelagh and Tysoe, Carolyn and Noh, Grace and Tarnopolsky, Mark and Brady, Lauren and Zafar, Muhammad and Schrier Vergano, Samantha A and Murray, Brianna and Sawyer, Lindsey and Hainline, Bryan E and Sapp, Katherine and DeMarzo, Danielle and Huismann, Darcy J and Wentzensen, Ingrid M and Schnur, Rhonda E and Monaghan, Kristin G and Juusola, Jane and Rhodes, Lindsay and Dobyns, William B and Lecoquierre, Francois and Goldenberg, Alice and Polster, Tilman and Axer-Schaefer, Susanne and Platzer, Konrad and Kl{\"o}ckner, Chiara and Hoffman, Trevor L and MacArthur, Daniel G and O{\textquoteright}Leary, Melanie C and VanNoy, Grace E and England, Eleina and Varghese, Vinod C and Mefford, Heather C} } @article {943, title = {Expanding the disease phenotype of ADSSL1-associated myopathy in non-Korean patients.}, journal = {Neuromuscul Disord}, volume = {30}, year = {2020}, month = {2020 04}, pages = {310-314}, abstract = {

Adenylosuccinate synthase (ADSSL1) is a muscle specific enzyme involved in the purine nucleotide cycle and responsible for the conversion of inosine monophosphate to adenosine monophosphate. Since 2016, when mutations in the ADSSL1 gene were first described to be associated with an adult onset distal myopathy, nine patients with compound heterozygous variants in the ADSSL1 gene, all of Korean origin, have been identified. Here we report a novel ADSSL1 mutation and describe two sporadic cases of Turkish and Indian origin. Many of the clinical features of both patients and muscle histopathology and muscle MRI findings, were in accordance with previously reported findings in the adult onset distal myopathy individuals. However, one of our patients presented with progressive, proximally pronounced weakness, severe muscle atrophy and early contractures. Thus, mutations in ADSSL1 have to be considered in patients with both distal and proximal muscle weakness and across various ethnicities.

}, issn = {1873-2364}, doi = {10.1016/j.nmd.2020.02.006}, author = {Mroczek, Magdalena and Durmus, Hacer and Bijarnia-MAHy, Sunita and Topf, Ana and Ghaoui, Roula and Bryen, Samantha and Duff, Jennifer and England, Eleina and Cooper, Sandra T and MacArthur, Daniel G and Straub, Volker} } @article {764, title = {The genetic and clinical landscape of nanophthalmos and posterior microphthalmos in an Australian cohort.}, journal = {Clin Genet}, volume = {97}, year = {2020}, month = {2020 05}, pages = {764-769}, abstract = {

Nanophthalmos and posterior microphthalmos are ocular abnormalities in which both eyes are abnormally small, and typically associated with extreme hyperopia. We recruited 40 individuals from 13 kindreds with nanophthalmos or posterior microphthalmos, with 12 probands subjected to exome sequencing. Nine probands (69.2\%) were assigned a genetic diagnosis, with variants in MYRF, TMEM98, MFRP, and PRSS56. Two of four PRSS56 families harbored the previously described c.1066dupC variant implicated in over half of all reported PRSS56 kindreds, with different surrounding haplotypes in each family suggesting a mutational hotspot. Individuals with a genetic diagnosis had shorter mean axial lengths and higher hyperopia than those without, with recessive forms associated with the most extreme phenotypes. These findings detail the genetic architecture of nanophthalmos and posterior microphthalmos in a cohort of predominantly European ancestry, their relative clinical phenotypes, and highlight the shared genetic architecture of rare and common disorders of refractive error.

}, issn = {1399-0004}, doi = {10.1111/cge.13722}, author = {Siggs, Owen M and Awadalla, Mona S and Souzeau, Emmanuelle and Staffieri, Sandra E and Kearns, Lisa S and Laurie, Kate and Kuot, AbrAHm and Qassim, Ayub and Edwards, Thomas L and Coote, Michael A and Mancel, Erica and Walland, Mark J and Dondey, Joanne and Galanopoulous, Anna and Casson, Robert J and Mills, Richard A and MacArthur, Daniel G and Ruddle, Jonathan B and Burdon, Kathryn P and Craig, Jamie E} } @article {785, title = {Landscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes.}, journal = {Nat Commun}, volume = {11}, year = {2020}, month = {2020 05 27}, pages = {2539}, abstract = {

Multi-nucleotide variants (MNVs), defined as two or more nearby variants existing on the same haplotype in an individual, are a clinically and biologically important class of genetic variation. However, existing tools typically do not accurately classify MNVs, and understanding of their mutational origins remains limited. Here, we systematically survey MNVs in 125,748 whole exomes and 15,708 whole genomes from the Genome Aggregation Database (gnomAD). We identify 1,792,248 MNVs across the genome with constituent variants falling within 2 bp distance of one another, including 18,756 variants with a novel combined effect on protein sequence. Finally, we estimate the relative impact of known mutational mechanisms - CpG deamination, replication error by polymerase zeta, and polymerase slippage at repeat junctions - on the generation of MNVs. Our results demonstrate the value of haplotype-aware variant annotation, and refine our understanding of genome-wide mutational mechanisms of MNVs.

}, keywords = {CpG Islands, Databases, Genetic, DNA Mutational Analysis, Exome, Genetic Variation, Genome, Human, Humans, Mutation}, issn = {2041-1723}, doi = {10.1038/s41467-019-12438-5}, author = {Wang, Qingbo and Pierce-Hoffman, Emma and Cummings, Beryl B and Alf{\"o}ldi, Jessica and Francioli, Laurent C and Gauthier, Laura D and Hill, Andrew J and O{\textquoteright}Donnell-Luria, Anne H and Karczewski, Konrad J and MacArthur, Daniel G} } @article {784, title = {The mutational constraint spectrum quantified from variation in 141,456 humans.}, journal = {Nature}, volume = {581}, year = {2020}, month = {2020 05}, pages = {434-443}, abstract = {

Genetic variants that inactivate protein-coding genes are a powerful source of information about the phenotypic consequences of gene disruption: genes that are crucial for the function of an organism will be depleted of such variants in natural populations, whereas non-essential genes will tolerate their accumulation. However, predicted loss-of-function variants are enriched for annotation errors, and tend to be found at extremely low frequencies, so their analysis requires careful variant annotation and very large sample sizes. Here we describe the aggregation of 125,748 exomes and 15,708 genomes from human sequencing studies into the Genome Aggregation Database (gnomAD). We identify 443,769 high-confidence predicted loss-of-function variants in this cohort after filtering for artefacts caused by sequencing and annotation errors. Using an improved model of human mutation rates, we classify human protein-coding genes along a spectrum that represents tolerance to inactivation, validate this classification using data from model organisms and engineered human cells, and show that it can be used to improve the power of gene discovery for both common and rare diseases.

}, keywords = {Adult, Brain, Cardiovascular Diseases, Cohort Studies, Databases, Genetic, Exome, Female, Genes, Essential, Genetic Predisposition to Disease, Genetic Variation, Genome, Human, Genome-Wide Association Study, Humans, Loss of Function Mutation, Male, Mutation Rate, Proprotein Convertase 9, Reproducibility of Results, RNA, Messenger, Whole Exome Sequencing, Whole Genome Sequencing}, issn = {1476-4687}, doi = {10.1038/s41586-020-2308-7}, author = {Karczewski, Konrad J and Francioli, Laurent C and Tiao, Grace and Cummings, Beryl B and Alf{\"o}ldi, Jessica and Wang, Qingbo and Collins, Ryan L and Laricchia, Kristen M and Ganna, Andrea and Birnbaum, Daniel P and Gauthier, Laura D and Brand, Harrison and Solomonson, Matthew and Watts, Nicholas A and Rhodes, Daniel and Singer-Berk, Moriel and England, Eleina M and Seaby, Eleanor G and Kosmicki, Jack A and Walters, Raymond K and Tashman, Katherine and Farjoun, Yossi and Banks, Eric and Poterba, Timothy and Wang, Arcturus and Seed, Cotton and Whiffin, Nicola and Chong, Jessica X and Samocha, Kaitlin E and Pierce-Hoffman, Emma and Zappala, Zachary and O{\textquoteright}Donnell-Luria, Anne H and Minikel, Eric Vallabh and Weisburd, Ben and Lek, Monkol and Ware, James S and Vittal, Christopher and Armean, Irina M and Bergelson, Louis and Cibulskis, Kristian and Connolly, Kristen M and Covarrubias, Miguel and Donnelly, Stacey and Ferriera, Steven and Gabriel, Stacey and Gentry, Jeff and Gupta, Namrata and Jeandet, Thibault and Kaplan, Diane and Llanwarne, Christopher and Munshi, Ruchi and Novod, Sam and Petrillo, Nikelle and Roazen, David and Ruano-Rubio, Valentin and Saltzman, Andrea and Schleicher, Molly and Soto, Jose and Tibbetts, Kathleen and Tolonen, Charlotte and Wade, Gordon and Talkowski, Michael E and Neale, Benjamin M and Daly, Mark J and MacArthur, Daniel G} } @article {907, title = {Mutations of the Transcriptional Corepressor ZMYM2 Cause Syndromic Urinary Tract Malformations.}, journal = {Am J Hum Genet}, volume = {107}, year = {2020}, month = {2020 10 01}, pages = {727-742}, abstract = {

Congenital anomalies of the kidney and urinary tract (CAKUT) constitute one of the most frequent birth defects and represent the most common cause of chronic kidney disease in the first three decades of life. Despite the discovery of dozens of monogenic causes of CAKUT, most pathogenic pathways remain elusive. We performed whole-exome sequencing (WES) in 551 individuals with CAKUT and identified a heterozygous de novo stop-gain variant in ZMYM2 in two different families with CAKUT. Through collaboration, we identified in total 14 different heterozygous loss-of-function mutations in ZMYM2 in 15 unrelated families. Most mutations occurred de novo, indicating possible interference with reproductive function. Human disease features are replicated in X.~tropicalis larvae with morpholino knockdowns, in which expression of truncated ZMYM2 proteins, based on individual mutations, failed to rescue renal and craniofacial defects. Moreover, heterozygous Zmym2-deficient mice recapitulated features of CAKUT with high penetrance. The ZMYM2 protein is a component of a transcriptional corepressor complex recently linked to the silencing of developmentally regulated endogenous retrovirus elements. Using protein-protein interaction assays, we show that ZMYM2 interacts with additional epigenetic silencing complexes, as well as confirming that it binds to FOXP1, a transcription factor that has also been linked to CAKUT. In summary, our findings establish that loss-of-function mutations of ZMYM2, and potentially that of other proteins in its interactome, as causes of human CAKUT, offering new routes for studying the pathogenesis of the disorder.

}, keywords = {Amphibian Proteins, Animals, Case-Control Studies, Child, Child, Preschool, DNA-Binding Proteins, Epigenesis, Genetic, Family, Female, Forkhead Transcription Factors, Heterozygote, Humans, Infant, Larva, Male, Mice, Mice, Knockout, Morpholinos, Mutation, Pedigree, Protein Binding, Repressor Proteins, Transcription Factors, Urinary Tract, Urogenital Abnormalities, Whole Exome Sequencing, Xenopus}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2020.08.013}, author = {Connaughton, Dervla M and Dai, Rufeng and Owen, Danielle J and Marquez, Jonathan and Mann, Nina and GrAHm-Paquin, Adda L and Nakayama, Makiko and Coyaud, Etienne and Laurent, Estelle M N and St-Germain, Jonathan R and Blok, Lot Snijders and Vino, Arianna and Kl{\"a}mbt, Verena and Deutsch, Konstantin and Wu, Chen-Han Wilfred and Kolvenbach, Caroline M and Kause, Franziska and Ottlewski, Isabel and Schneider, Ronen and Kitzler, Thomas M and Majmundar, Amar J and Buerger, Florian and Onuchic-Whitford, Ana C and Youying, Mao and Kolb, Amy and Salmanullah, Daanya and Chen, Evan and van der Ven, Amelie T and Rao, Jia and Ityel, Hadas and Seltzsam, Steve and Rieke, Johanna M and Chen, Jing and Vivante, Asaf and Hwang, Daw-Yang and Kohl, Stefan and Dworschak, Gabriel C and Hermle, Tobias and Alders, Marielle and Bartolomaeus, Tobias and Bauer, Stuart B and Baum, Michelle A and Brilstra, Eva H and Challman, Thomas D and Zyskind, Jacob and Costin, Carrie E and Dipple, Katrina M and Duijkers, Floor A and Ferguson, Marcia and FitzPatrick, David R and Fick, Roger and Glass, Ian A and Hulick, Peter J and Kline, Antonie D and Krey, Ilona and Kumar, Selvin and Lu, Weining and Marco, Elysa J and Wentzensen, Ingrid M and Mefford, Heather C and Platzer, Konrad and Povolotskaya, Inna S and Savatt, Juliann M and Shcherbakova, Natalia V and Senguttuvan, Prabha and Squire, Audrey E and Stein, Deborah R and Thiffault, Isabelle and Voinova, Victoria Y and Somers, Michael J G and Ferguson, Michael A and Traum, Avram Z and Daouk, Ghaleb H and Daga, Ankana and Rodig, Nancy M and Terhal, Paulien A and van Binsbergen, Ellen and Eid, Loai A and Tasic, Velibor and Rasouly, Hila Milo and Lim, Tze Y and Ahram, Dina F and Gharavi, Ali G and Reutter, Heiko M and Rehm, Heidi L and MacArthur, Daniel G and Lek, Monkol and Laricchia, Kristen M and Lifton, Richard P and Xu, Hong and Mane, Shrikant M and Sanna-Cherchi, Simone and Sharrocks, Andrew D and Raught, Brian and Fisher, Simon E and Bouchard, Maxime and Khokha, Mustafa K and Shril, Shirlee and Hildebrandt, Friedhelm} } @article {713, title = {Recurrent TTN metatranscript-only c.39974-11T>G splice variant associated with autosomal recessive arthrogryposis multiplex congenita and myopathy.}, journal = {Hum Mutat}, volume = {41}, year = {2020}, month = {2020 02}, pages = {403-411}, abstract = {

We present eight families with arthrogryposis multiplex congenita and myopathy bearing a TTN intron 213 extended splice-site variant (NM_001267550.1:c.39974-11T>G), inherited in trans with a second pathogenic TTN variant. Muscle-derived RNA studies of three individuals confirmed mis-splicing induced by the c.39974-11T>G variant; in-frame exon 214 skipping or use of a cryptic 3{\textquoteright} splice-site effecting a frameshift. Confounding interpretation of pathogenicity is the absence of exons 213-217 within the described skeletal muscle TTN N2A isoform. However, RNA-sequencing from 365 adult human gastrocnemius samples revealed that 56\% specimens predominantly include exons 213-217 in TTN transcripts (inclusion rate >=66\%). Further, RNA-sequencing of five fetal muscle samples confirmed that 4/5 specimens predominantly include exons 213-217 (fifth sample inclusion rate 57\%). Contractures improved significantly with age for four individuals, which may be linked to decreased expression of pathogenic fetal transcripts. Our study extends emerging evidence supporting a vital developmental role for TTN isoforms containing metatranscript-only exons.

}, issn = {1098-1004}, doi = {10.1002/humu.23938}, author = {Bryen, Samantha J and Ewans, Lisa J and Pinner, Jason and MacLennan, Suzanna C and Donkervoort, Sandra and Castro, Diana and Topf, Ana and O{\textquoteright}Grady, Gina and Cummings, Beryl and Chao, Katherine R and Weisburd, Ben and Francioli, Laurent and Faiz, Fathimath and Bournazos, Adam M and Hu, Ying and Grosmann, Carla and Malicki, Denise M and Doyle, Helen and Witting, Nanna and Vissing, John and Claeys, Kristl G and Urankar, Kathryn and Beleza-Meireles, Ana and Baptista, Julia and Ellard, Sian and Savarese, Marco and Johari, Mridul and Vihola, Anna and Udd, Bjarne and Majumdar, Anirban and Straub, Volker and B{\"o}nnemann, Carsten G and MacArthur, Daniel G and Davis, Mark R and Cooper, Sandra T} } @article {911, title = {Sequential targeted exome sequencing of 1001 patients affected by unexplained limb-girdle weakness.}, journal = {Genet Med}, volume = {22}, year = {2020}, month = {2020 09}, pages = {1478-1488}, abstract = {

PURPOSE: Several hundred genetic muscle diseases have been described, all of which are rare. Their clinical and genetic heterogeneity means that a genetic diagnosis is challenging. We established an international consortium, MYO-SEQ, to aid the work-ups of muscle disease patients and to better understand disease etiology.

METHODS: Exome sequencing was applied to 1001 undiagnosed patients recruited from more than 40 neuromuscular disease referral centers; standardized phenotypic information was collected for each patient. Exomes were examined for variants in 429 genes associated with muscle conditions.

RESULTS: We identified suspected pathogenic variants in 52\% of patients across 87 genes. We detected 401 novel variants, 116 of which were recurrent. Variants in CAPN3, DYSF, ANO5, DMD, RYR1, TTN, COL6A2, and SGCA collectively accounted for over half of the solved cases; while variants in newer disease genes, such as BVES and POGLUT1, were also found. The remaining well-characterized unsolved patients (48\%) need further investigation.

CONCLUSION: Using our unique infrastructure, we developed a pathway to expedite muscle disease diagnoses. Our data suggest that exome sequencing should be used for pathogenic variant detection in patients with suspected genetic muscle diseases, focusing first on the most common disease genes described here, and subsequently in rarer and newly characterized disease genes.

}, keywords = {Anoctamins, Exome, Glucosyltransferases, Humans, Muscular Dystrophies, Limb-Girdle, Whole Exome Sequencing}, issn = {1530-0366}, doi = {10.1038/s41436-020-0840-3}, author = {Topf, Ana and Johnson, Katherine and Bates, Adam and Phillips, Lauren and Chao, Katherine R and England, Eleina M and Laricchia, Kristen M and Mullen, Thomas and Valkanas, Elise and Xu, Liwen and Bertoli, Marta and Blain, Alison and Casas{\'u}s, Ana B and Duff, Jennifer and Mroczek, Magdalena and Specht, Sabine and Lek, Monkol and Ensini, Monica and MacArthur, Daniel G and Straub, Volker} } @article {755, title = {Severe neurodevelopmental disease caused by a homozygous TLK2 variant.}, journal = {Eur J Hum Genet}, volume = {28}, year = {2020}, month = {2020 03}, pages = {383-387}, abstract = {

A distinct neurodevelopmental phenotype characterised mainly by mild motor and language delay and facial dysmorphism, caused by heterozygous de novo or dominant variants in the TLK2 gene has recently been described. All cases reported carried either truncating variants located throughout the gene, or missense changes principally located at the C-terminal end of the protein mostly resulting in haploinsufficiency of TLK2. Through whole exome sequencing, we identified a homozygous missense variant in TLK2 in a patient showing more severe symptoms than those previously described, including cerebellar vermis hypoplasia and West syndrome. Both parents are heterozygous for the variant and clinically unaffected highlighting that recessive variants in TLK2 can also be disease causing and may act through a different pathomechanism.

}, keywords = {Adult, Cerebellum, Child, Developmental Disabilities, Female, Heterozygote, Homozygote, Humans, Infant, Male, Mutation, Missense, Nervous System Malformations, Pedigree, Protein Kinases, Spasms, Infantile}, issn = {1476-5438}, doi = {10.1038/s41431-019-0519-x}, author = {Topf, Ana and Oktay, Yavuz and Balaraju, Sunitha and Yilmaz, Elmasnur and Sonmezler, Ece and Yis, Uluc and Laurie, Steven and Thompson, Rachel and Roos, Andreas and MacArthur, Daniel G and Yaramis, Ahmet and G{\"u}ng{\"o}r, Serdal and Lochm{\"u}ller, Hanns and Hiz, Semra and Horvath, Rita} } @article {836, title = {A structural variation reference for medical and population genetics.}, journal = {Nature}, volume = {581}, year = {2020}, month = {2020 05}, pages = {444-451}, abstract = {

Structural variants (SVs) rearrange large segments of DNA and can have profound consequences in evolution and human disease. As national biobanks, disease-association studies, and clinical genetic testing have grown increasingly reliant on genome sequencing, population references such as the Genome Aggregation Database (gnomAD) have become integral in the interpretation of single-nucleotide variants (SNVs). However, there are no reference maps of SVs from high-coverage genome sequencing comparable to those for SNVs. Here we present a reference of sequence-resolved SVs constructed from 14,891 genomes across diverse global populations (54\% non-European) in gnomAD. We discovered a rich and complex landscape of 433,371 SVs, from which we estimate that SVs are responsible for 25-29\% of all rare protein-truncating events per genome. We found strong correlations between natural selection against damaging SNVs and rare SVs that disrupt or duplicate protein-coding sequence, which suggests that genes that are highly intolerant to loss-of-function are also sensitive to increased dosage. We also uncovered modest selection against noncoding SVs in cis-regulatory elements, although selection against protein-truncating SVs was stronger than all noncoding effects. Finally, we identified very large (over one megabase), rare SVs in 3.9\% of samples, and estimate that 0.13\% of individuals may carry an SV that meets the existing criteria for clinically important incidental findings. This SV resource is freely distributed via the gnomAD browser and will have broad utility in population genetics, disease-association studies, and diagnostic screening.

}, keywords = {Continental Population Groups, Disease, Female, Genetic Testing, Genetic Variation, Genetics, Medical, Genetics, Population, Genome, Human, Genotyping Techniques, Humans, Male, Middle Aged, Mutation, Polymorphism, Single Nucleotide, Reference Standards, Selection, Genetic, Whole Genome Sequencing}, issn = {1476-4687}, doi = {10.1038/s41586-020-2287-8}, author = {Collins, Ryan L and Brand, Harrison and Karczewski, Konrad J and Zhao, Xuefang and Alf{\"o}ldi, Jessica and Francioli, Laurent C and Khera, Amit V and Lowther, Chelsea and Gauthier, Laura D and Wang, Harold and Watts, Nicholas A and Solomonson, Matthew and O{\textquoteright}Donnell-Luria, Anne and Baumann, Alexander and Munshi, Ruchi and Walker, Mark and Whelan, Christopher W and Huang, Yongqing and Brookings, Ted and Sharpe, Ted and Stone, Matthew R and Valkanas, Elise and Fu, Jack and Tiao, Grace and Laricchia, Kristen M and Ruano-Rubio, Valentin and Stevens, Christine and Gupta, Namrata and Cusick, Caroline and Margolin, Lauren and Taylor, Kent D and Lin, Henry J and Rich, Stephen S and Post, Wendy S and Chen, Yii-Der Ida and Rotter, Jerome I and Nusbaum, Chad and Philippakis, Anthony and Lander, Eric and Gabriel, Stacey and Neale, Benjamin M and Kathiresan, Sekar and Daly, Mark J and Banks, Eric and MacArthur, Daniel G and Talkowski, Michael E} } @article {732, title = {The Genetic Landscape of Diamond-Blackfan Anemia.}, journal = {Am J Hum Genet}, volume = {104}, year = {2019}, month = {2019 Feb 07}, pages = {356}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2018.12.011}, author = {Ulirsch, Jacob C and Verboon, Jeffrey M and Kazerounian, Shideh and Guo, Michael H and Yuan, Daniel and Ludwig, Leif S and Handsaker, Robert E and Abdulhay, Nour J and Fiorini, Claudia and Genovese, Giulio and Lim, Elaine T and Cheng, Aaron and Cummings, Beryl B and Chao, Katherine R and Beggs, Alan H and Genetti, Casie A and Sieff, Colin A and Newburger, Peter E and Niewiadomska, Edyta and Matysiak, Michal and Vlachos, Adrianna and Lipton, Jeffrey M and Atsidaftos, Eva and Glader, Bertil and Narla, Anupama and Gleizes, Pierre-Emmanuel and O{\textquoteright}Donohue, Marie-Fran{\c c}oise and Montel-Lehry, Nathalie and Amor, David J and McCarroll, Steven A and O{\textquoteright}Donnell-Luria, Anne H and Gupta, Namrata and Gabriel, Stacey B and MacArthur, Daniel G and Lander, Eric S and Lek, Monkol and Da Costa, Lydie and Nathan, David G and Korostelev, Andrei A and Do, Ron and Sankaran, Vijay G and Gazda, Hanna T} } @article {706, title = {Genetic regulatory variation in populations informs transcriptome analysis in rare disease.}, journal = {Science}, volume = {366}, year = {2019}, month = {2019 10 18}, pages = {351-356}, abstract = {

Transcriptome data can facilitate the interpretation of the effects of rare genetic variants. Here, we introduce ANEVA (analysis of expression variation) to quantify genetic variation in gene dosage from allelic expression (AE) data in a population. Application of ANEVA to the Genotype-Tissues Expression (GTEx) data showed that this variance estimate is robust and correlated with selective constraint in a gene. Using these variance estimates in a dosage outlier test (ANEVA-DOT) applied to AE data from 70 Mendelian muscular disease patients showed accuracy in detecting genes with pathogenic variants in previously resolved cases and led to one confirmed and several potential new diagnoses. Using our reference estimates from GTEx data, ANEVA-DOT can be incorporated in rare disease diagnostic pipelines to use RNA-sequencing data more effectively.

}, issn = {1095-9203}, doi = {10.1126/science.aay0256}, author = {Mohammadi, Pejman and Castel, Stephane E and Cummings, Beryl B and Einson, Jonah and Sousa, Christina and Hoffman, Paul and Donkervoort, Sandra and Jiang, Zhuoxun and Mohassel, Payam and Foley, A Reghan and Wheeler, Heather E and Im, Hae Kyung and B{\"o}nnemann, Carsten G and MacArthur, Daniel G and Lappalainen, Tuuli} } @article {595, title = {Insights into genetics, human biology and disease gleaned from family based genomic studies.}, journal = {Genet Med}, volume = {21}, year = {2019}, month = {2019 04}, pages = {798-812}, abstract = {

Identifying genes and variants contributing to rare disease phenotypes and Mendelian conditions informs biology and medicine, yet potential phenotypic consequences for variation of >75\% of the ~20,000 annotated genes in the human genome are lacking. Technical advances to assess rare variation genome-wide, particularly exome sequencing (ES), enabled establishment in the United States of the National Institutes of Health (NIH)-supported Centers for Mendelian Genomics (CMGs) and have facilitated collaborative studies resulting in~novel "disease gene" discoveries. Pedigree-based genomic studies and rare variant analyses in families with suspected Mendelian conditions have led to the elucidation of hundreds of novel disease genes and highlighted the impact of de novo mutational events, somatic variation underlying nononcologic traits, incompletely penetrant alleles, phenotypes with high locus heterogeneity, and multilocus pathogenic variation. Herein, we highlight CMG collaborative discoveries that have contributed to understanding both rare and common diseases and discuss opportunities for future discovery in single-locus Mendelian disorder genomics. Phenotypic annotation of all human genes; development of bioinformatic tools and analytic methods; exploration of non-Mendelian modes of inheritance including reduced penetrance, multilocus variation, and oligogenic inheritance; construction of allelic series at a locus; enhanced data sharing worldwide; and integration with clinical genomics are explored. Realizing the full contribution of rare disease research to functional annotation of the human genome, and further illuminating human biology and health, will lay the foundation for the Precision Medicine Initiative.

}, keywords = {Databases, Genetic, Genetic Diseases, Inborn, Genetic Heterogeneity, Genetic Predisposition to Disease, Genome, Human, Genomics, Humans, National Institutes of Health (U.S.), Pedigree, United States, Whole Exome Sequencing}, issn = {1530-0366}, doi = {10.1038/s41436-018-0408-7}, author = {Posey, Jennifer E and O{\textquoteright}Donnell-Luria, Anne H and Chong, Jessica X and Harel, Tamar and Jhangiani, Shalini N and Coban Akdemir, Zeynep H and Buyske, Steven and Pehlivan, Davut and Carvalho, Claudia M B and Baxter, Samantha and Sobreira, Nara and Liu, Pengfei and Wu, Nan and Rosenfeld, Jill A and Kumar, Sushant and Avramopoulos, Dimitri and White, Janson J and Doheny, Kimberly F and Witmer, P Dane and Boehm, Corinne and Sutton, V Reid and Muzny, Donna M and Boerwinkle, Eric and G{\"u}nel, Murat and Nickerson, Deborah A and Mane, Shrikant and MacArthur, Daniel G and Gibbs, Richard A and Hamosh, Ada and Lifton, Richard P and Matise, Tara C and Rehm, Heidi L and Gerstein, Mark and Bamshad, Michael J and Valle, David and Lupski, James R} } @article {688, title = {Pathogenic Abnormal Splicing Due to Intronic Deletions that Induce Biophysical Space Constraint for Spliceosome Assembly.}, journal = {Am J Hum Genet}, volume = {105}, year = {2019}, month = {2019 Sep 05}, pages = {573-587}, abstract = {

A precise genetic diagnosis is the single most important step for families with genetic disorders to enable personalized and preventative medicine. In addition to genetic variants in coding regions (exons) that can change a protein sequence, abnormal pre-mRNA splicing can be devastating for the encoded protein, inducing a frameshift or in-frame deletion/insertion of multiple residues. Non-coding variants that disrupt splicing are extremely challenging to identify. Stemming from an initial clinical discovery in two index Australian families, we define 25 families with genetic disorders caused by a class of pathogenic non-coding splice variant due to intronic deletions. These pathogenic intronic deletions spare all consensus splice motifs, though they critically shorten the minimal distance between the 5{\textquoteright} splice-site (5{\textquoteright}SS) and branchpoint. The mechanistic basis for abnormal splicing is due to biophysical constraint precluding U1/U2 spliceosome assembly, which stalls in A-complexes (that bridge the 5{\textquoteright}SS and branchpoint). Substitution of deleted nucleotides with non-specific sequences restores spliceosome assembly and normal splicing, arguing against loss of an intronic element as the primary causal basis. Incremental lengthening of 5{\textquoteright}SS-branchpoint length in our index EMD case subject defines 45-47 nt as the critical elongation enabling (inefficient) spliceosome assembly for EMD intron 5. The 5{\textquoteright}SS-branchpoint space constraint mechanism, not currently factored by genomic informatics pipelines, is relevant to diagnosis and precision medicine across the breadth of Mendelian disorders and cancer genomics.

}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2019.07.013}, author = {Bryen, Samantha J and Joshi, Himanshu and Evesson, Frances J and Girard, Cyrille and Ghaoui, Roula and Waddell, Leigh B and Testa, Alison C and Cummings, Beryl and Arbuckle, Susan and Graf, Nicole and Webster, Richard and MacArthur, Daniel G and Laing, Nigel G and Davis, Mark R and L{\"u}hrmann, Reinhard and Cooper, Sandra T} } @article {649, title = {Recessive DES cardio/myopathy without myofibrillar aggregates: intronic splice variant silences one allele leaving only missense L190P-desmin.}, journal = {Eur J Hum Genet}, volume = {27}, year = {2019}, month = {2019 Aug}, pages = {1267-1273}, abstract = {

We establish autosomal recessive DES variants p.(Leu190Pro) and a deep intronic splice variant causing inclusion of a frameshift-inducing artificial exon/intronic fragment, as the likely cause of myopathy with cardiac involvement in female siblings. Both sisters presented in their twenties with slowly progressive limb girdle weakness, severe systolic dysfunction, and progressive, severe respiratory weakness. Desmin is an intermediate filament protein typically associated with autosomal dominant myofibrillar myopathy with cardiac involvement. However a few rare cases of autosomal recessive desminopathy are reported. In this family, a paternal missense p.(Leu190Pro) variant was viewed unlikely to be causative of autosomal dominant desminopathy, as the father and brothers carrying this variant were clinically unaffected. Clinical fit with a DES-related myopathy encouraged closer scrutiny of all DES variants, identifying a maternal deep intronic variant within intron-7, predicted to create a cryptic splice site, which segregated with disease. RNA sequencing and studies of muscle cDNA confirmed the deep intronic variant caused aberrant splicing of an artificial exon/intronic fragment into maternal DES mRNA transcripts, encoding a premature termination codon, and potently activating nonsense-mediate decay (92\% paternal DES transcripts, 8\% maternal). Western blot showed 60-75\% reduction in desmin levels, likely comprised only of missense p.(Leu190Pro) desmin. Biopsy showed fibre size variation with increased central nuclei. Electron microscopy showed extensive myofibrillar disarray, duplication of the basal lamina, but no inclusions or aggregates. This study expands the phenotypic spectrum of recessive DES cardio/myopathy, and emphasizes the continuing importance of muscle biopsy for functional genomics pursuit of {\textquoteright}tricky{\textquoteright} variants in neuromuscular conditions.

}, issn = {1476-5438}, doi = {10.1038/s41431-019-0393-6}, author = {Riley, Lisa G and Waddell, Leigh B and Ghaoui, Roula and Evesson, Frances J and Cummings, Beryl B and Bryen, Samantha J and Joshi, Himanshu and Wang, Min-Xia and Brammah, Susan and Kritharides, Leonard and Corbett, Alastair and MacArthur, Daniel G and Cooper, Sandra T} } @article {655, title = {A recurrent COL6A1 pseudoexon insertion causes muscular dystrophy and is effectively targeted by splice-correction therapies.}, journal = {JCI Insight}, volume = {4}, year = {2019}, month = {2019 Mar 21}, abstract = {

The clinical application of advanced next-generation sequencing technologies is increasingly uncovering novel classes of mutations that may serve as potential targets for precision medicine therapeutics. Here, we show that a deep intronic splice defect in the COL6A1 gene, originally discovered by applying muscle RNA sequencing in patients with clinical findings of collagen VI-related dystrophy (COL6-RD), inserts an in-frame pseudoexon into COL6A1 mRNA, encodes a mutant collagen α1(VI) protein that exerts a dominant-negative effect on collagen VI matrix assembly, and provides a unique opportunity for splice-correction approaches aimed at restoring normal gene expression. Using splice-modulating antisense oligomers, we efficiently skipped the pseudoexon in patient-derived fibroblast cultures and restored a wild-type matrix. Similarly, we used CRISPR/Cas9 to precisely delete an intronic sequence containing the pseudoexon and efficiently abolish its inclusion while preserving wild-type splicing. Considering that this splice defect is emerging as one of the single most frequent mutations in COL6-RD, the design of specific and effective splice-correction therapies offers a promising path for clinical translation.

}, issn = {2379-3708}, doi = {10.1172/jci.insight.124403}, author = {Bolduc, Veronique and Foley, A Reghan and Solomon-Degefa, Herimela and Sarathy, Apurva and Donkervoort, Sandra and Hu, Ying and Chen, Grace S and Sizov, Katherine and Nalls, Matthew and Zhou, Haiyan and Aguti, Sara and Cummings, Beryl B and Lek, Monkol and Tukiainen, Taru and Marshall, Jamie L and Regev, Oded and Marek-Yagel, Dina and Sarkozy, Anna and Butterfield, Russell J and Jou, Cristina and Jimenez-Mallebrera, Cecilia and Li, Yan and Gartioux, Corine and Mamchaoui, Kamel and Allamand, Val{\'e}rie and Gualandi, Francesca and Ferlini, Alessandra and Hanssen, Eric and Wilton, Steve D and Lamand{\'e}, Shireen R and MacArthur, Daniel G and Wagener, Raimund and Muntoni, Francesco and B{\"o}nnemann, Carsten G} } @article {502, title = { and Mutations Implicate RAB5 Regulation in Nephrotic Syndrome.}, journal = {J Am Soc Nephrol}, volume = {29}, year = {2018}, month = {2018 Aug}, pages = {2123-2138}, abstract = {

BACKGROUND: Steroid-resistant nephrotic syndrome (SRNS) is a frequent cause of CKD. The discovery of monogenic causes of SRNS has revealed specific pathogenetic pathways, but these monogenic causes do not explain all cases of SRNS.

METHODS: To identify novel monogenic causes of SRNS, we screened 665 patients by whole-exome sequencing. We then evaluated the functional significance of two genes and the mutations therein that we discovered through this sequencing and conducted complementary studies in podocyte-like nephrocytes.

RESULTS: We identified conserved, homozygous missense mutations of in two families with early-onset NS and a homozygous missense mutation of in two siblings with SRNS. GAPVD1 and ANKFY1 interact with the endosomal regulator RAB5. Coimmunoprecipitation assays indicated interaction between GAPVD1 and ANKFY1 proteins, which also colocalized when expressed in HEK293T cells. Silencing either protein diminished the podocyte migration rate. Compared with wild-type GAPVD1 and ANKFY1, the mutated proteins produced upon ectopic expression of or bearing the patient-derived mutations exhibited altered binding affinity for active RAB5 and reduced ability to rescue the knockout-induced defect in podocyte migration. Coimmunoprecipitation assays further demonstrated a physical interaction between nephrin and GAPVD1, and immunofluorescence revealed partial colocalization of these proteins in rat glomeruli. The patient-derived mutations reduced nephrin-GAPVD1 binding affinity. In , silencing impaired endocytosis and caused mistrafficking of the nephrin ortholog.

CONCLUSIONS: Mutations in and probably in are novel monogenic causes of NS. The discovery of these genes implicates RAB5 regulation in the pathogenesis of human NS.

}, issn = {1533-3450}, doi = {10.1681/ASN.2017121312}, author = {Hermle, Tobias and Schneider, Ronen and Schapiro, David and Braun, Daniela A and van der Ven, Amelie T and Warejko, Jillian K and Daga, Ankana and Widmeier, Eugen and Nakayama, Makiko and Jobst-Schwan, Tilman and Majmundar, Amar J and Ashraf, Shazia and Rao, Jia and Finn, Laura S and Tasic, Velibor and Hernandez, Joel D and Bagga, Arvind and Jalalah, Sawsan M and El Desoky, Sherif and Kari, Jameela A and Laricchia, Kristen M and Lek, Monkol and Rehm, Heidi L and MacArthur, Daniel G and Mane, Shrikant and Lifton, Richard P and Shril, Shirlee and Hildebrandt, Friedhelm} } @article {451, title = {Congenital Titinopathy: Comprehensive characterization and pathogenic insights.}, journal = {Ann Neurol}, volume = {83}, year = {2018}, month = {2018 Jun}, pages = {1105-1124}, abstract = {

OBJECTIVE: Comprehensive clinical characterization of congenital titinopathy to facilitate diagnosis and management of this important emerging disorder.

METHODS: Using massively parallel sequencing we identified 30 patients from 27 families with 2 pathogenic nonsense, frameshift and/or splice site TTN mutations in trans. We then undertook a detailed analysis of the clinical, histopathological and imaging features of these patients.

RESULTS: All patients had prenatal or early onset hypotonia and/or congenital contractures. None had ophthalmoplegia. Scoliosis and respiratory insufficiency typically developed early and progressed rapidly, whereas limb weakness was often slowly progressive, and usually did not prevent independent walking. Cardiac involvement was present in 46\% of patients. Relatives of 2 patients had dilated cardiomyopathy. Creatine kinase levels were normal to moderately elevated. Increased fiber size variation, internalized nuclei and cores were common histopathological abnormalities. Cap-like regions, whorled or ring fibers, and mitochondrial accumulations were also observed. Muscle magnetic resonance imaging showed gluteal, hamstring and calf muscle involvement. Western blot analysis showed a near-normal sized titin protein in all samples. The presence of 2 mutations predicted to impact both N2BA and N2B cardiac isoforms appeared to be associated with greatest risk of cardiac involvement. One-third of patients had 1 mutation predicted to impact exons present in fetal skeletal muscle, but not included within the mature skeletal muscle isoform transcript. This strongly suggests developmental isoforms are involved in the pathogenesis of this congenital/early onset disorder.

INTERPRETATION: This detailed clinical reference dataset will greatly facilitate diagnostic confirmation and management of patients, and has provided important insights into disease pathogenesis. Ann Neurol 2018;83:1105-1124.

}, issn = {1531-8249}, doi = {10.1002/ana.25241}, author = {Oates, Emily C and Jones, Kristi J and Donkervoort, Sandra and Charlton, Amanda and Brammah, Susan and Smith, John E and Ware, James S and Yau, Kyle S and Swanson, Lindsay C and Whiffin, Nicola and Peduto, Anthony J and Bournazos, Adam and Waddell, Leigh B and Farrar, Michelle A and Sampaio, Hugo A and Teoh, Hooi Ling and Lamont, Phillipa J and Mowat, David and Fitzsimons, Robin B and Corbett, Alastair J and Ryan, Monique M and O{\textquoteright}Grady, Gina L and Sandaradura, Sarah A and Ghaoui, Roula and Joshi, Himanshu and Marshall, Jamie L and Nolan, Melinda A and Kaur, Simranpreet and Punetha, Jaya and Topf, Ana and Harris, Elizabeth and Bakshi, Madhura and Genetti, Casie A and Marttila, Minttu and Werlauff, Ulla and Streichenberger, Nathalie and Pestronk, Alan and Mazanti, Ingrid and Pinner, Jason R and Vuillerot, Carole and Grosmann, Carla and Camacho, Ana and Mohassel, Payam and Leach, Meganne E and Foley, A Reghan and Bharucha-Goebel, Diana and Collins, James and Connolly, Anne M and Gilbreath, Heather R and Iannaccone, Susan T and Castro, Diana and Cummings, Beryl B and Webster, Richard I and Lazaro, Le{\"\i}la and Vissing, John and Coppens, Sandra and Deconinck, Nicolas and Luk, Ho-Ming and Thomas, Neil H and Foulds, Nicola C and Illingworth, Marjorie A and Ellard, Sian and McLean, Catriona A and Phadke, Rahul and Ravenscroft, Gianina and Witting, Nanna and Hackman, Peter and Richard, Isabelle and Cooper, Sandra T and Kamsteeg, Erik-Jan and Hoffman, Eric P and Bushby, Kate and Straub, Volker and Udd, Bjarne and Ferreiro, Ana and North, Kathryn N and Clarke, Nigel F and Lek, Monkol and Beggs, Alan H and B{\"o}nnemann, Carsten G and MacArthur, Daniel G and Granzier, Henk and Davis, Mark R and Laing, Nigel G} } @article {487, title = {Detection of variants in dystroglycanopathy-associated genes through the application of targeted whole-exome sequencing analysis to a large cohort of patients with unexplained limb-girdle muscle weakness.}, journal = {Skelet Muscle}, volume = {8}, year = {2018}, month = {2018 07 30}, pages = {23}, abstract = {

BACKGROUND: Dystroglycanopathies are a clinically and genetically heterogeneous group of disorders that are typically characterised by limb-girdle muscle weakness. Mutations in 18 different genes have been associated with dystroglycanopathies, the encoded proteins of which typically modulate the binding of α-dystroglycan to extracellular matrix ligands by altering its glycosylation. This results in a disruption of the structural integrity of the myocyte, ultimately leading to muscle degeneration.

METHODS: Deep phenotypic information was gathered using the PhenoTips online software for 1001 patients with unexplained limb-girdle muscle weakness from 43 different centres across 21 European and Middle Eastern countries. Whole-exome sequencing with at least 250~ng DNA was completed using an Illumina exome capture and a 38~Mb baited target. Genes known to be associated with dystroglycanopathies were analysed for disease-causing variants.

RESULTS: Suspected pathogenic variants were detected in DPM3, ISPD, POMT1 and FKTN in one patient each, in POMK in two patients, in GMPPB in three patients, in FKRP in eight patients and in POMT2 in ten patients. This indicated a frequency of 2.7\% for the disease group within the cohort of 1001 patients with unexplained limb-girdle muscle weakness. The phenotypes of the 27 patients were highly variable, yet with a fundamental presentation of proximal muscle weakness and elevated serum creatine kinase.

CONCLUSIONS: Overall, we have identified 27 patients with suspected pathogenic variants in dystroglycanopathy-associated genes. We present evidence for the genetic and phenotypic diversity of the dystroglycanopathies as a disease group, while also highlighting the advantage of incorporating next-generation sequencing into the diagnostic pathway of rare diseases.

}, keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Child, Child, Preschool, Dystroglycans, Female, Genetic Predisposition to Disease, Genetic Variation, Glycosylation, Heterozygote, Homozygote, Humans, Male, Middle Aged, Muscle Proteins, Muscular Dystrophies, Limb-Girdle, Mutation, Phenotype, Whole Exome Sequencing, Young Adult}, issn = {2044-5040}, doi = {10.1186/s13395-018-0170-1}, author = {Johnson, Katherine and Bertoli, Marta and Phillips, Lauren and Topf, Ana and Van den Bergh, Peter and Vissing, John and Witting, Nanna and Nafissi, Shahriar and Jamal-Omidi, Shirin and {\L}usakowska, Anna and Kostera-Pruszczyk, Anna and Potulska-Chromik, Anna and Deconinck, Nicolas and Wallgren-Pettersson, Carina and Strang-Karlsson, Sonja and Colomer, Jaume and Claeys, Kristl G and De Ridder, Willem and Baets, Jonathan and von der Hagen, Maja and Fern{\'a}ndez-Torr{\'o}n, Roberto and Zulaica Ijurco, Miren and Espinal Valencia, Juan Bautista and Hahn, Andreas and Durmus, Hacer and Willis, Tracey and Xu, Liwen and Valkanas, Elise and Mullen, Thomas E and Lek, Monkol and MacArthur, Daniel G and Straub, Volker} } @article {578, title = {The Genetic Landscape of Diamond-Blackfan Anemia.}, journal = {Am J Hum Genet}, volume = {103}, year = {2018}, month = {2018 12 06}, pages = {930-947}, abstract = {

Diamond-Blackfan anemia (DBA) is a rare bone marrow failure disorder that affects 7 out of 1,000,000 live births and has been associated with mutations in components of the ribosome. In order to characterize the genetic landscape of this heterogeneous disorder, we recruited a cohort of 472 individuals with a clinical diagnosis of DBA and performed whole-exome sequencing (WES). We identified relevant rare and predicted damaging mutations for 78\% of individuals. The majority of mutations were singletons, absent from population databases, predicted to cause loss of function, and located in 1 of 19 previously reported ribosomal protein (RP)-encoding genes. Using exon coverage estimates, we identified and validated 31 deletions in RP genes. We also observed an enrichment for extended splice site mutations and validated their diverse effects using RNA sequencing in cell lines obtained from individuals with DBA. Leveraging the size of our cohort, we observed robust genotype-phenotype associations with congenital abnormalities and treatment outcomes. We further identified rare mutations in seven previously unreported RP genes that may cause DBA, as well as several distinct disorders that appear to phenocopy DBA, including nine individuals with biallelic CECR1 mutations that result in deficiency of ADA2. However, no new genes were identified at exome-wide significance, suggesting that there are no unidentified genes containing mutations readily identified by WES that explain >5\% of DBA-affected case subjects. Overall, this report should inform not only clinical practice for DBA-affected individuals, but also the design and analysis of rare variant studies for heterogeneous Mendelian disorders.

}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2018.10.027}, author = {Ulirsch, Jacob C and Verboon, Jeffrey M and Kazerounian, Shideh and Guo, Michael H and Yuan, Daniel and Ludwig, Leif S and Handsaker, Robert E and Abdulhay, Nour J and Fiorini, Claudia and Genovese, Giulio and Lim, Elaine T and Cheng, Aaron and Cummings, Beryl B and Chao, Katherine R and Beggs, Alan H and Genetti, Casie A and Sieff, Colin A and Newburger, Peter E and Niewiadomska, Edyta and Matysiak, Michal and Vlachos, Adrianna and Lipton, Jeffrey M and Atsidaftos, Eva and Glader, Bertil and Narla, Anupama and Gleizes, Pierre-Emmanuel and O{\textquoteright}Donohue, Marie-Fran{\c c}oise and Montel-Lehry, Nathalie and Amor, David J and McCarroll, Steven A and O{\textquoteright}Donnell-Luria, Anne H and Gupta, Namrata and Gabriel, Stacey B and MacArthur, Daniel G and Lander, Eric S and Lek, Monkol and Da Costa, Lydie and Nathan, David G and Korostelev, Andrei A and Do, Ron and Sankaran, Vijay G and Gazda, Hanna T} } @article {511, title = {matchbox: An open-source tool for patient matching via the Matchmaker Exchange.}, journal = {Hum Mutat}, volume = {39}, year = {2018}, month = {2018 Dec}, pages = {1827-1834}, abstract = {

Rare disease investigators constantly face challenges in identifying additional cases to build evidence for gene-disease causality. The Matchmaker Exchange (MME) addresses this limitation by providing a mechanism for matching patients across genomic centers via a federated network. The MME has revolutionized searching for additional cases by making it possible to query across institutional boundaries, so that what was once a laborious and manual process of contacting researchers is now automated and computable. However, while the MME network is beginning to scale, the growth of additional nodes is limited by the lack of easy-to-use solutions that can be implemented by any rare disease database owner, even one without significant software engineering resources. Here, we describe matchbox, which is an open-source, platform-independent, portable bridge between any given rare disease genomic center and the MME network, which has already led to novel gene discoveries. We also describe how matchbox greatly reduces the barrier to participation by overcoming challenges for new databases to join the MME.

}, issn = {1098-1004}, doi = {10.1002/humu.23655}, author = {Arachchi, Harindra and Wojcik, Monica H and Weisburd, Benjamin and Jacobsen, Julius O B and Valkanas, Elise and Baxter, Samantha and Byrne, Alicia B and O{\textquoteright}Donnell-Luria, Anne H and Haendel, Melissa and Smedley, Damian and MacArthur, Daniel G and Philippakis, Anthony A and Rehm, Heidi L} } @article {432, title = {Nemaline myopathy and distal arthrogryposis associated with an autosomal recessive~TNNT3~splice variant.}, journal = {Hum Mutat}, volume = {39}, year = {2018}, month = {2018 03}, pages = {383-388}, abstract = {

A male neonate presented with severe weakness, hypotonia, contractures and congenital scoliosis. Skeletal muscle specimens showed marked atrophy and degeneration of fast fibers with striking nemaline rods and hypertrophy of slow fibers that were ultrastructurally normal. A neuromuscular gene panel identified a homozygous essential splice variant in TNNT3 (chr11:1956150G~>~A, NM_006757.3:c.681+1G~>~A). TNNT3 encodes skeletal troponin-T and is associated with autosomal dominant distal arthrogryposis. TNNT3 has not previously been associated with nemaline myopathy (NM), a rare congenital myopathy linked to defects in proteins associated with thin filament structure and regulation. cDNA studies confirmed pathogenic consequences of the splice variant, eliciting exon-skipping and intron retention events leading to a frameshift. Western blot showed deficiency of troponin-T protein with secondary loss of troponin-I . We establish a homozygous splice variant in TNNT3 as the likely cause of severe congenital NM with distal arthrogryposis, characterized by specific involvement of Type-2 fibers and deficiency of troponin-T .

}, keywords = {Arthrogryposis, Genes, Recessive, Humans, Infant, Infant, Newborn, Male, Myopathies, Nemaline, RNA Splice Sites, RNA Splicing, RNA, Messenger, Troponin T}, issn = {1098-1004}, doi = {10.1002/humu.23385}, author = {Sandaradura, Sarah A and Bournazos, Adam and Mallawaarachchi, Amali and Cummings, Beryl B and Waddell, Leigh B and Jones, Kristi J and Troedson, Christopher and Sudarsanam, Annapurna and Nash, Benjamin M and Peters, Gregory B and Algar, Elizabeth M and MacArthur, Daniel G and North, Kathryn N and Brammah, Susan and Charlton, Amanda and Laing, Nigel G and Wilson, Meredith J and Davis, Mark R and Cooper, Sandra T} } @article {501, title = {STRetch: detecting and discovering pathogenic short tandem repeat expansions.}, journal = {Genome Biol}, volume = {19}, year = {2018}, month = {2018 08 21}, pages = {121}, abstract = {

Short tandem repeat (STR) expansions have been identified as the causal DNA mutation in dozens of Mendelian diseases. Most existing tools for detecting STR variation with short reads do so within the read length and so are unable to detect the majority of pathogenic expansions. Here we present STRetch, a new genome-wide method to scan for STR expansions at all loci across the human genome. We demonstrate the use of STRetch for detecting STR expansions using short-read whole-genome sequencing data at known pathogenic loci as well as novel STR loci. STRetch is open source software, available from github.com/Oshlack/STRetch .

}, keywords = {Alleles, Chromosomes, Human, DNA Repeat Expansion, Genetic Loci, Genome, Human, Humans, Microsatellite Repeats, Polymerase Chain Reaction, Software}, issn = {1474-760X}, doi = {10.1186/s13059-018-1505-2}, author = {Dashnow, Harriet and Lek, Monkol and Phipson, Belinda and Halman, Andreas and Sadedin, Simon and Lonsdale, Andrew and Davis, Mark and Lamont, Phillipa and Clayton, Joshua S and Laing, Nigel G and MacArthur, Daniel G and Oshlack, Alicia} } @article {516, title = {Whole-Exome Sequencing Identifies Causative Mutations in Families with Congenital Anomalies of the Kidney and Urinary Tract.}, journal = {J Am Soc Nephrol}, volume = {29}, year = {2018}, month = {2018 Sep}, pages = {2348-2361}, abstract = {

BACKGROUND: Congenital anomalies of the kidney and urinary tract (CAKUT) are the most prevalent cause of kidney disease in the first three decades of life. Previous gene panel studies showed monogenic causation in up to 12\% of patients with CAKUT.

METHODS: We applied whole-exome sequencing to analyze the genotypes of individuals from 232 families with CAKUT, evaluating for mutations in single genes known to cause human CAKUT and genes known to cause CAKUT in mice. In consanguineous or multiplex families, we additionally performed a search for novel monogenic causes of CAKUT.

RESULTS: In 29 families (13\%), we detected a causative mutation in a known gene for isolated or syndromic CAKUT that sufficiently explained the patient{\textquoteright}s CAKUT phenotype. In three families (1\%), we detected a mutation in a gene reported to cause a phenocopy of CAKUT. In 15 of 155 families with isolated CAKUT, we detected deleterious mutations in syndromic CAKUT genes. Our additional search for novel monogenic causes of CAKUT in consanguineous and multiplex families revealed a potential single, novel monogenic CAKUT gene in 19 of 232 families (8\%).

CONCLUSIONS: We identified monogenic mutations in a known human CAKUT gene or CAKUT phenocopy gene as the cause of disease in 14\% of the CAKUT families in this study. Whole-exome sequencing provides an etiologic diagnosis in a high fraction of patients with CAKUT and will provide a new basis for the mechanistic understanding of CAKUT.

}, issn = {1533-3450}, doi = {10.1681/ASN.2017121265}, author = {van der Ven, Amelie T and Connaughton, Dervla M and Ityel, Hadas and Mann, Nina and Nakayama, Makiko and Chen, Jing and Vivante, Asaf and Hwang, Daw-Yang and Schulz, Julian and Braun, Daniela A and Schmidt, Johanna Magdalena and Schapiro, David and Schneider, Ronen and Warejko, Jillian K and Daga, Ankana and Majmundar, Amar J and Tan, Weizhen and Jobst-Schwan, Tilman and Hermle, Tobias and Widmeier, Eugen and Ashraf, Shazia and Amar, Ali and Hoogstraaten, Charlotte A and Hugo, Hannah and Kitzler, Thomas M and Kause, Franziska and Kolvenbach, Caroline M and Dai, Rufeng and Spaneas, Leslie and Amann, Kassaundra and Stein, Deborah R and Baum, Michelle A and Somers, Michael J G and Rodig, Nancy M and Ferguson, Michael A and Traum, Avram Z and Daouk, Ghaleb H and Bogdanovic, Radovan and Staji{\'c}, Natasa and Soliman, Neveen A and Kari, Jameela A and El Desoky, Sherif and Fathy, Hanan M and Milosevic, Danko and Al-Saffar, Muna and Awad, Hazem S and Eid, Loai A and Selvin, Aravind and Senguttuvan, Prabha and Sanna-Cherchi, Simone and Rehm, Heidi L and MacArthur, Daniel G and Lek, Monkol and Laricchia, Kristen M and Wilson, Michael W and Mane, Shrikant M and Lifton, Richard P and Lee, Richard S and Bauer, Stuart B and Lu, Weining and Reutter, Heiko M and Tasic, Velibor and Shril, Shirlee and Hildebrandt, Friedhelm} } @article {421, title = {Identification of GAA variants through whole exome sequencing targeted to a cohort of 606 patients with unexplained limb-girdle muscle weakness.}, journal = {Orphanet J Rare Dis}, volume = {12}, year = {2017}, month = {2017 11 17}, pages = {173}, abstract = {

BACKGROUND: Late-onset Pompe disease is a rare genetic neuromuscular disorder caused by a primary deficiency of α-glucosidase and the associated accumulation of glycogen in lysosomal vacuoles. The deficiency of α-glucosidase can often be detected using an inexpensive and readily accessible dried blood spot test when Pompe disease is suspected. Like several neuromuscular disorders, Pompe disease typically presents with progressive weakness of limb-girdle muscles and respiratory insufficiency. Due to the phenotypic heterogeneity of these disorders, however, it is often difficult for clinicians to reach a diagnosis for patients with Pompe disease. Six hundred and six patients from a European population were recruited onto our study. Inclusion criteria stipulated that index cases must present with limb-girdle weakness or elevated serum creatine kinase activity. Whole exome sequencing with at least 250~ng DNA was completed using an Illumina exome capture and a 38~Mb baited target. A panel of 169 candidate genes for limb-girdle weakness was analysed for disease-causing variants.

RESULTS: A total of 35 variants within GAA were detected. Ten distinct variants in eight unrelated index cases (and four siblings not sequenced in our study) were considered disease-causing, with the patients presenting with heterogeneous phenotypes. The eight unrelated individuals were compound heterozygotes for two variants. Six patients carried the intronic splice site c.-13~T > G transversion and two of the six patients also carried the exonic p.Glu176ArgfsTer45 frameshift. Four of the ten variants were novel in their association with Pompe disease.

CONCLUSIONS: Here, we highlight the advantage of using whole exome sequencing as a tool for detecting, diagnosing and treating patients with rare, clinically variable genetic disorders.

}, keywords = {Adolescent, Adult, Aged, Aged, 80 and over, alpha-Glucosidases, Child, Child, Preschool, Cohort Studies, Female, Genetic Variation, Glycogen Storage Disease Type II, Humans, Male, Middle Aged, Muscle Weakness, Muscular Dystrophies, Limb-Girdle, Whole Exome Sequencing, Young Adult}, issn = {1750-1172}, doi = {10.1186/s13023-017-0722-1}, author = {Johnson, Katherine and Topf, Ana and Bertoli, Marta and Phillips, Lauren and Claeys, Kristl G and Stojanovic, Vidosava Rakocevic and Peri{\'c}, Stojan and Hahn, Andreas and Maddison, Paul and Akay, Ela and Bastian, Alexandra E and {\L}usakowska, Anna and Kostera-Pruszczyk, Anna and Lek, Monkol and Xu, Liwen and MacArthur, Daniel G and Straub, Volker} } @article {364, title = {Improving genetic diagnosis in Mendelian disease with transcriptome sequencing.}, journal = {Sci Transl Med}, volume = {9}, year = {2017}, month = {2017 04 19}, abstract = {

Exome and whole-genome sequencing are becoming increasingly routine approaches in Mendelian disease diagnosis. Despite their success, the current diagnostic rate for genomic analyses across a variety of rare diseases is approximately 25 to 50\%. We explore the utility of transcriptome sequencing [RNA sequencing (RNA-seq)] as a complementary diagnostic tool in a cohort of 50 patients with genetically undiagnosed rare muscle disorders. We describe an integrated approach to analyze patient muscle RNA-seq, leveraging an analysis framework focused on the detection of transcript-level changes that are unique to the patient compared to more than 180 control skeletal muscle samples. We demonstrate the power of RNA-seq to validate candidate splice-disrupting mutations and to identify splice-altering variants in both exonic and deep intronic regions, yielding an overall diagnosis rate of 35\%. We also report the discovery of a highly recurrent de novo intronic mutation in that results in a dominantly acting splice-gain event, disrupting the critical glycine repeat motif of the triple helical domain. We identify this pathogenic variant in a total of 27 genetically unsolved patients in an external collagen VI-like dystrophy cohort, thus explaining approximately 25\% of patients clinically suggestive of having collagen VI dystrophy in whom prior genetic analysis is negative. Overall, this study represents a large systematic application of transcriptome sequencing to rare disease diagnosis and highlights its utility for the detection and interpretation of variants missed by current standard diagnostic approaches.

}, keywords = {Collagen Type VI, High-Throughput Nucleotide Sequencing, Humans, Muscular Diseases, Mutation, Transcriptome}, issn = {1946-6242}, doi = {10.1126/scitranslmed.aal5209}, author = {Cummings, Beryl B and Marshall, Jamie L and Tukiainen, Taru and Lek, Monkol and Donkervoort, Sandra and Foley, A Reghan and Bolduc, Veronique and Waddell, Leigh B and Sandaradura, Sarah A and O{\textquoteright}Grady, Gina L and Estrella, Elicia and Reddy, Hemakumar M and Zhao, Fengmei and Weisburd, Ben and Karczewski, Konrad J and O{\textquoteright}Donnell-Luria, Anne H and Birnbaum, Daniel and Sarkozy, Anna and Hu, Ying and Gonorazky, Hernan and Claeys, Kristl and Joshi, Himanshu and Bournazos, Adam and Oates, Emily C and Ghaoui, Roula and Davis, Mark R and Laing, Nigel G and Topf, Ana and Kang, Peter B and Beggs, Alan H and North, Kathryn N and Straub, Volker and Dowling, James J and Muntoni, Francesco and Clarke, Nigel F and Cooper, Sandra T and B{\"o}nnemann, Carsten G and MacArthur, Daniel G} } @article {17, title = {The sensitivity of exome sequencing in identifying pathogenic mutations for LGMD in the United States.}, journal = {J Hum Genet}, volume = {62}, year = {2017}, month = {2017 Feb}, pages = {243-252}, abstract = {

The current study characterizes a cohort of limb-girdle muscular dystrophy (LGMD) in the United States using whole-exome sequencing. Fifty-five families affected by LGMD were recruited using an institutionally approved protocol. Exome sequencing was performed on probands and selected parental samples. Pathogenic mutations and cosegregation patterns were confirmed by Sanger sequencing. Twenty-two families (40\%) had novel and previously reported pathogenic mutations, primarily in LGMD genes, and also in genes for Duchenne muscular dystrophy, facioscapulohumeral muscular dystrophy, congenital myopathy, myofibrillar myopathy, inclusion body myopathy and Pompe disease. One family was diagnosed via clinical testing. Dominant mutations were identified in COL6A1, COL6A3, FLNC, LMNA, RYR1, SMCHD1 and VCP, recessive mutations in ANO5, CAPN3, GAA, LAMA2, SGCA and SGCG, and X-linked mutations in DMD. A previously reported variant in DMD was confirmed to be benign. Exome sequencing is a powerful diagnostic tool for LGMD. Despite careful phenotypic screening, pathogenic mutations were found in other muscle disease genes, largely accounting for the increased sensitivity of exome sequencing. Our experience suggests that broad sequencing panels are useful for these analyses because of the phenotypic overlap of many neuromuscular conditions. The confirmation of a benign DMD variant illustrates the potential of exome sequencing to help determine pathogenicity.

}, keywords = {Base Sequence, Distal Myopathies, Exome, Female, Genetic Testing, Glycogen Storage Disease Type II, Humans, Male, Muscular Dystrophies, Limb-Girdle, Muscular Dystrophy, Duchenne, Muscular Dystrophy, Facioscapulohumeral, Mutation, Myopathies, Structural, Congenital, Sequence Analysis, DNA, United States}, issn = {1435-232X}, doi = {10.1038/jhg.2016.116}, author = {Reddy, Hemakumar M and Cho, Kyung-Ah and Lek, Monkol and Estrella, Elicia and Valkanas, Elise and Jones, Michael D and Mitsuhashi, Satomi and Darras, Basil T and Amato, Anthony A and Lidov, Hart Gw and Brownstein, Catherine A and Margulies, David M and Yu, Timothy W and Salih, Mustafa A and Kunkel, Louis M and MacArthur, Daniel G and Kang, Peter B} } @article {28, title = {De Novo Mutations in SON Disrupt RNA Splicing of Genes Essential for Brain Development and Metabolism, Causing an Intellectual-Disability Syndrome.}, journal = {Am J Hum Genet}, volume = {99}, year = {2016}, month = {2016 Sep 01}, pages = {711-719}, abstract = {

The overall understanding of the molecular etiologies of intellectual disability (ID) and developmental delay (DD) is increasing as next-generation sequencing technologies identify genetic variants in individuals with such disorders. However, detailed analyses conclusively confirming these variants, as well as the underlying molecular mechanisms explaining the diseases, are often lacking. Here, we report on an ID syndrome caused by de novo heterozygous loss-of-function (LoF) mutations in SON. The syndrome is characterized by ID and/or DD, malformations of the cerebral cortex, epilepsy, vision problems, musculoskeletal abnormalities, and congenital malformations. Knockdown of son in zebrafish resulted in severe malformation of the spine, brain, and eyes. Importantly, analyses of RNA from affected individuals revealed that genes critical for neuronal migration and cortex organization (TUBG1, FLNA, PNKP, WDR62, PSMD3, and~HDAC6) and metabolism (PCK2, PFKL, IDH2, ACY1, and ADA) are significantly downregulated because of the accumulation of mis-spliced transcripts resulting from erroneous SON-mediated RNA splicing. Our data highlight SON as a master regulator governing neurodevelopment and demonstrate the importance of SON-mediated RNA splicing in human development.

}, keywords = {Animals, Brain, Developmental Disabilities, DNA-Binding Proteins, Eye Abnormalities, Female, Genes, Essential, Haploinsufficiency, Head, Heterozygote, Humans, Intellectual Disability, Male, Metabolic Diseases, Minor Histocompatibility Antigens, Mutation, Pedigree, RNA Splicing, RNA, Messenger, Spine, Syndrome, Zebrafish}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2016.06.029}, author = {Kim, Jung-Hyun and Shinde, Deepali N and Reijnders, Margot R F and Hauser, Natalie S and Belmonte, Rebecca L and Wilson, Gregory R and Bosch, Dani{\"e}lle G M and Bubulya, Paula A and Shashi, Vandana and Petrovski, Slav{\'e} and Stone, Joshua K and Park, Eun Young and Veltman, Joris A and Sinnema, Margje and Stumpel, Connie T R M and Draaisma, Jos M and Nicolai, Joost and Yntema, Helger G and Lindstrom, Kristin and de Vries, Bert B A and Jewett, Tamison and Santoro, Stephanie L and Vogt, Julie and Bachman, Kristine K and Seeley, Andrea H and Krokosky, Alyson and Turner, Clesson and Rohena, Luis and Hempel, Maja and Kort{\"u}m, Fanny and Lessel, Davor and Neu, Axel and Strom, Tim M and Wieczorek, Dagmar and Bramswig, Nuria and Laccone, Franco A and Behunova, Jana and Rehder, Helga and Gordon, Christopher T and Rio, Marl{\`e}ne and Romana, Serge and Tang, Sha and El-Khechen, Dima and Cho, Megan T and McWalter, Kirsty and Douglas, Ganka and Baskin, Berivan and Begtrup, Amber and Funari, Tara and Schoch, Kelly and Stegmann, Alexander P A and Stevens, Servi J C and Zhang, Dong-Er and Traver, David and Yao, Xu and MacArthur, Daniel G and Brunner, Han G and Mancini, Grazia M and Myers, Richard M and Owen, Laurie B and Lim, Ssang-Taek and Stachura, David L and Vissers, Lisenka E L M and Ahn, Eun-Young Erin} } @article {534, title = {Variants in SLC18A3, vesicular acetylcholine transporter, cause congenital myasthenic syndrome.}, journal = {Neurology}, volume = {87}, year = {2016}, month = {2016 Oct 04}, pages = {1442-1448}, abstract = {

OBJECTIVE: To describe the clinical and genetic characteristics of presynaptic congenital myasthenic syndrome secondary to biallelic variants in SLC18A3.

METHODS: Individuals from 2 families were identified with biallelic variants in SLC18A3, the gene encoding the vesicular acetylcholine transporter (VAChT), through whole-exome sequencing.

RESULTS: The patients demonstrated features seen in presynaptic congenital myasthenic syndrome, including ptosis, ophthalmoplegia, fatigable weakness, apneic crises, and deterioration of symptoms in cold water for patient 1. Both patients demonstrated moderate clinical improvement on pyridostigmine. Patient 1 had a broader phenotype, including learning difficulties and left ventricular dysfunction. Electrophysiologic studies were typical for a presynaptic defect. Both patients showed profound electrodecrement on low-frequency repetitive stimulation followed by a prolonged period of postactivation exhaustion. In patient 1, this was unmasked only after isometric contraction, a recognized feature of presynaptic disease, emphasizing the importance of activation procedures.

CONCLUSIONS: VAChT is responsible for uptake of acetylcholine into presynaptic vesicles. The clinical and electrographic characteristics of the patients described are consistent with previously reported mouse models of VAChT deficiency. These findings make it very likely that defects in VAChT due to variants in SLC18A3 are a cause of congenital myasthenic syndrome in humans.

}, keywords = {Adolescent, Child, Diagnosis, Differential, Female, Genetic Variation, Humans, Male, Myasthenic Syndromes, Congenital, Vesicular Acetylcholine Transport Proteins}, issn = {1526-632X}, doi = {10.1212/WNL.0000000000003179}, author = {O{\textquoteright}Grady, Gina L and Verschuuren, Corien and Yuen, Michaela and Webster, Richard and Menezes, Manoj and Fock, Johanna M and Pride, Natalie and Best, Heather A and Benavides Damm, Tatiana and Turner, Christian and Lek, Monkol and Engel, Andrew G and North, Kathryn N and Clarke, Nigel F and MacArthur, Daniel G and Kamsteeg, Erik-Jan and Cooper, Sandra T} } @article {455, title = {Variants in the Oxidoreductase PYROXD1 Cause Early-Onset Myopathy with Internalized Nuclei and Myofibrillar Disorganization.}, journal = {Am J Hum Genet}, volume = {99}, year = {2016}, month = {2016 Nov 03}, pages = {1086-1105}, abstract = {

This study establishes PYROXD1 variants as a cause of early-onset myopathy and uses biospecimens and cell lines, yeast, and zebrafish models to elucidate the fundamental role of PYROXD1 in skeletal muscle. Exome sequencing identified recessive variants in PYROXD1 in nine probands from five families. Affected individuals presented in infancy or childhood with slowly progressive proximal and distal weakness, facial weakness, nasal speech, swallowing difficulties, and normal to moderately elevated creatine kinase. Distinctive histopathology showed abundant internalized nuclei, myofibrillar disorganization, desmin-positive inclusions, and thickened Z-bands. PYROXD1 is a nuclear-cytoplasmic pyridine nucleotide-disulphide reductase (PNDR). PNDRs are flavoproteins (FAD-binding) and catalyze pyridine-nucleotide-dependent (NAD/NADH) reduction of thiol residues in other proteins. Complementation experiments in yeast lacking glutathione reductase glr1 show that human PYROXD1 has reductase activity that is strongly impaired by the disease-associated missense mutations. Immunolocalization studies in human muscle and zebrafish myofibers demonstrate that PYROXD1 localizes to the nucleus and to striated sarcomeric compartments. Zebrafish with ryroxD1 knock-down recapitulate features of PYROXD1 myopathy with sarcomeric disorganization, myofibrillar aggregates, and marked swimming defect. We characterize variants in the oxidoreductase PYROXD1 as a cause of early-onset myopathy with distinctive histopathology and introduce altered redox regulation as a primary cause of congenital muscle disease.

}, keywords = {Amino Acid Sequence, Animals, Cell Nucleus, Cercopithecus aethiops, Cohort Studies, COS Cells, Creatine Kinase, Cytoplasm, Distal Myopathies, ELAV-Like Protein 4, Female, Flavoproteins, Gene Deletion, Genetic Variation, Genome-Wide Association Study, Glutathione Reductase, HEK293 Cells, Humans, Male, Muscle, Skeletal, Mutation, Missense, Myopathies, Structural, Congenital, Oxidoreductases, Pedigree, Protein Conformation, Saccharomyces cerevisiae Proteins, Zebrafish}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2016.09.005}, author = {O{\textquoteright}Grady, Gina L and Best, Heather A and Sztal, Tamar E and Schartner, Vanessa and Sanjuan-Vazquez, Myriam and Donkervoort, Sandra and Abath Neto, Osorio and Sutton, Roger Bryan and Ilkovski, Biljana and Romero, Norma Beatriz and Stojkovic, Tanya and Dastgir, Jahannaz and Waddell, Leigh B and Boland, Anne and Hu, Ying and Williams, Caitlin and Ruparelia, Avnika A and Maisonobe, Thierry and Peduto, Anthony J and Reddel, Stephen W and Lek, Monkol and Tukiainen, Taru and Cummings, Beryl B and Joshi, Himanshu and Nectoux, Juliette and Brammah, Susan and Deleuze, Jean-Fran{\c c}ois and Ing, Viola Oorschot and Ramm, Georg and Ardicli, Didem and Nowak, Kristen J and Talim, Beril and Topaloglu, Haluk and Laing, Nigel G and North, Kathryn N and MacArthur, Daniel G and Friant, Sylvie and Clarke, Nigel F and Bryson-Richardson, Robert J and B{\"o}nnemann, Carsten G and Laporte, Jocelyn and Cooper, Sandra T} }