@article {1004, title = {Exome sequencing reveals predominantly de novo variants in disorders with intellectual disability (ID) in the founder population of Finland.}, journal = {Hum Genet}, year = {2021}, month = {2021 Mar 12}, abstract = {

The genetics of autosomal recessive intellectual disability (ARID) has mainly been studied in consanguineous families, however, founder populations may also be of interest to study intellectual disability (ID) and the contribution of ARID. Here, we used a genotype-driven approach to study the genetic landscape of ID in the founder population of Finland. A total of 39 families with syndromic and non-syndromic ID were analyzed using exome sequencing, which revealed a variant in a known ID gene in 27 families. Notably, 75\% of these variants in known ID genes were de novo or suspected de novo (64\% autosomal dominant; 11\% X-linked) and 25\% were inherited (14\% autosomal recessive; 7\% X-linked; and 4\% autosomal dominant). A dual molecular diagnosis was suggested in two families (5\%). Via additional analysis and molecular testing, we identified three cases with an abnormal molecular karyotype, including chr21q22.12q22.2 uniparental disomy with a mosaic interstitial 2.7~Mb deletion covering DYRK1A and KCNJ6. Overall, a pathogenic or likely pathogenic variant was identified in 64\% (25/39) of the families. Last, we report an alternate inheritance model for 3 known ID genes (UBA7, DDX47, DHX58) and discuss potential candidate genes for ID, including SYPL1 and ERGIC3 with homozygous founder variants and de novo variants in POLR2F and DNAH3. In summary, similar to other European populations, de novo variants were the most common variants underlying ID in the studied Finnish population, with limited contribution of ARID to ID etiology, though mainly driven by founder and potential founder variation in the latter case.

}, issn = {1432-1203}, doi = {10.1007/s00439-021-02268-1}, author = {J{\"a}rvel{\"a}, Irma and M{\"a}{\"a}tt{\"a}, Tuomo and Acharya, Anushree and Lepp{\"a}l{\"a}, Juha and Jhangiani, Shalini N and Arvio, Maria and Siren, Auli and Kankuri-Tammilehto, Minna and Kokkonen, Hannaleena and Palom{\"a}ki, Maarit and Varilo, Teppo and Fang, Mary and Hadley, Trevor D and Jolly, Angad and Linnankivi, Tarja and Paetau, Ritva and Saarela, Anni and K{\"a}lvi{\"a}inen, Reetta and Olme, Jan and Nouel-Saied, Liz M and Cornejo-Sanchez, Diana M and Llaci, Lorida and Lupski, James R and Posey, Jennifer E and Leal, Suzanne M and Schrauwen, Isabelle} } @article {750, title = {Exome sequencing reveals a novel variant in causing intracranial aneurysm in a Chinese family.}, journal = {J Neurointerv Surg}, volume = {12}, year = {2020}, month = {2020 Feb}, pages = {221-226}, abstract = {

BACKGROUND: Genetic risk factors play an important role in the pathogenesis of familial intracranial aneurysms (FIAs); however, the molecular mechanisms remain largely unknown.

OBJECTIVE: To investigate potential FIA-causing genetic variants by rare variant interrogation and a family-based genomics approach in a large family with an extensive multigenerational pedigree with FIAs.

METHOD: Exome sequencing (ES) was performed in a dominant likely family with intracranial aneurysms (IAs). Variants were analyzed by an in-house developed pipeline and prioritized using various filtering strategies, including population frequency, variant type, and predicted variant pathogenicity. Sanger sequencing was also performed to evaluate the segregation of the variants with the phenotype.

RESULTS: Based on the ES data obtained from five individuals from a family with 7/21 living members affected with IAs, a total of 14 variants were prioritized as candidate variants. Familial segregation analysis revealed that c.2519T>C (p.Leu840Pro) segregated in accordance with Mendelian expectations with the phenotype within the family-that is, present in all IA-affected cases and absent from all unaffected members of the second generation. This missense variant is absent from public databases (1000genome, ExAC, gnomAD, ESP5400), and has damaging predictions by bioinformatics tools (Gerp ++ score = 5.88, CADD score = 16.43, MutationTaster score = 1, LRT score = 0). In addition, 840Leu in NFX1 is robustly conserved in mammals and maps in a region before the RING-type zinc finger domain.

CONCLUSION: c.2519T>C (p.Leu840Pro) may contribute to the pathogenetics of a subset of FIAs.

}, keywords = {Adult, Asian Continental Ancestry Group, Computational Biology, Exome, Female, Genetic Variation, Humans, Intracranial Aneurysm, Male, Middle Aged, Pedigree, Phenotype, Repressor Proteins}, issn = {1759-8486}, doi = {10.1136/neurintsurg-2019-014900}, author = {Ding, Xinghuan and Zhao, Sen and Zhang, Qianqian and Yan, Zihui and Wang, Yang and Wu, Yong and Li, Xiaoxin and Liu, Jian and Niu, Yuchen and Zhang, Yisen and Zhang, Mingqi and Wang, Huizi and Zhang, Ying and Chen, Weisheng and Yang, Xin-Zhuang and Liu, Pengfei and Posey, Jennifer E and Lupski, James R and Wu, Zhihong and Yang, Xinjian and Wu, Nan and Wang, Kun} } @article {680, title = {Exome Sequencing of a Primary Ovarian Insufficiency Cohort Reveals Common Molecular Etiologies for a Spectrum of Disease.}, journal = {J Clin Endocrinol Metab}, volume = {104}, year = {2019}, month = {2019 Aug 01}, pages = {3049-3067}, abstract = {

CONTEXT: Primary ovarian insufficiency (POI) encompasses a spectrum of premature menopause, including both primary and secondary amenorrhea. For 75\% to 90\% of individuals with hypergonadotropic hypogonadism presenting as POI, the molecular etiology is unknown. Common etiologies include chromosomal abnormalities, environmental factors, and congenital disorders affecting ovarian development and function, as well as syndromic and nonsyndromic single gene disorders suggesting POI represents a complex trait.

OBJECTIVE: To characterize the contribution of known disease genes to POI and identify molecular etiologies and biological underpinnings of POI.

DESIGN, SETTING, AND PARTICIPANTS: We applied exome sequencing (ES) and family-based genomics to 42 affected female individuals from 36 unrelated Turkish families, including 31 with reported parental consanguinity.

RESULTS: This analysis identified likely damaging, potentially contributing variants and molecular diagnoses in 16 families (44\%), including 11 families with likely damaging variants in known genes and five families with predicted deleterious variants in disease genes (IGSF10, MND1, MRPS22, and SOHLH1) not previously associated with POI. Of the 16 families, 2 (13\%) had evidence for potentially pathogenic variants at more than one locus. Absence of heterozygosity consistent with identity-by-descent mediated recessive disease burden contributes to molecular diagnosis in 15 of 16 (94\%) families. GeneMatcher allowed identification of additional families from diverse genetic backgrounds.

CONCLUSIONS: ES analysis of a POI cohort further characterized locus heterogeneity, reaffirmed the association of genes integral to meiotic recombination, demonstrated the likely contribution of genes involved in hypothalamic development, and documented multilocus pathogenic variation suggesting the potential for oligogenic inheritance contributing to the development of POI.

}, issn = {1945-7197}, doi = {10.1210/jc.2019-00248}, author = {Jolly, Angad and Bayram, Yavuz and Turan, Serap and Aycan, Zehra and Tos, Tulay and Abali, Zehra Yavas and Hacihamdioglu, Bulent and Coban Akdemir, Zeynep Hande and Hijazi, Hadia and Bas, Serpil and Atay, Zeynep and Guran, Tulay and Abali, Saygin and Bas, Firdevs and Darendeliler, Feyza and Colombo, Roberto and Barakat, Tahsin Stefan and Rinne, Tuula and White, Janson J and Yesil, G{\"o}zde and Gezdirici, Alper and Gulec, Elif Yilmaz and Karaca, Ender and Pehlivan, Davut and Jhangiani, Shalini N and Muzny, Donna M and Poyrazoglu, Sukran and Bereket, Abdullah and Gibbs, Richard A and Posey, Jennifer E and Lupski, James R} } @article {366, title = {Efficient CNV breakpoint analysis reveals unexpected structural complexity and correlation of dosage-sensitive genes with clinical severity in genomic disorders.}, journal = {Hum Mol Genet}, volume = {26}, year = {2017}, month = {2017 05 15}, pages = {1927-1941}, abstract = {

Genomic disorders are the clinical conditions manifested by submicroscopic genomic rearrangements including copy number variants (CNVs). The CNVs can be identified by array-based comparative genomic hybridization (aCGH), the most commonly used technology for molecular diagnostics of genomic disorders. However, clinical aCGH only informs CNVs in the probe-interrogated regions. Neither orientational information nor the resulting genomic rearrangement structure is provided, which is a key to uncovering mutational and pathogenic mechanisms underlying genomic disorders. Long-range polymerase chain reaction (PCR) is a traditional approach to obtain CNV breakpoint junction, but this method is inefficient when challenged by structural complexity such as often found at the PLP1 locus in association with Pelizaeus-Merzbacher disease (PMD). Here we introduced {\textquoteright}capture and single-molecule real-time sequencing{\textquoteright} (cap-SMRT-seq) and newly developed {\textquoteright}asymmetry linker-mediated nested PCR walking{\textquoteright} (ALN-walking) for CNV breakpoint sequencing in 49 subjects with PMD-associated CNVs. Remarkably, 29 (94\%) of the 31 CNV breakpoint junctions unobtainable by conventional long-range PCR were resolved by cap-SMRT-seq and ALN-walking. Notably, unexpected CNV complexities, including inter-chromosomal rearrangements that cannot be resolved by aCGH, were revealed by efficient breakpoint sequencing. These sequence-based structures of PMD-associated CNVs further support the role of DNA replicative mechanisms in CNV mutagenesis, and facilitate genotype-phenotype correlation studies. Intriguingly, the lengths of gained segments by CNVs are strongly correlated with clinical severity in PMD, potentially reflecting the functional contribution of other dosage-sensitive genes besides PLP1. Our study provides new efficient experimental approaches (especially ALN-walking) for CNV breakpoint sequencing and highlights their importance in uncovering CNV mutagenesis and pathogenesis in genomic disorders.

}, keywords = {Base Sequence, Comparative Genomic Hybridization, DNA Copy Number Variations, DNA Replication, Female, Gene Dosage, Gene Duplication, Gene Rearrangement, Genetic Association Studies, Genome, Human, Genomics, Humans, Male, Mutation, Pelizaeus-Merzbacher Disease, Sequence Analysis, DNA}, issn = {1460-2083}, doi = {10.1093/hmg/ddx102}, author = {Zhang, Ling and Wang, Jingmin and Zhang, Cheng and Li, Dongxiao and Carvalho, Claudia M B and Ji, Haoran and Xiao, Jianqiu and Wu, Ye and Zhou, Weichen and Wang, Hongyan and Jin, Li and Luo, Yang and Wu, Xiru and Lupski, James R and Zhang, Feng and Jiang, Yuwu} } @article {57, title = {Enrichment of mutations in chromatin regulators in people with Rett syndrome lacking mutations in MECP2.}, journal = {Genet Med}, volume = {19}, year = {2017}, month = {2017 01}, pages = {13-19}, abstract = {

PURPOSE: Rett syndrome (RTT) is a neurodevelopmental disorder caused primarily by de novo mutations in MECP2 and sometimes in CDKL5 and FOXG1. However, some RTT patients lack mutations in these genes.

METHODS: Twenty-two RTT patients without apparent MECP2, CDKL5, and FOXG1 mutations were subjected to both whole-exome sequencing and single-nucleotide polymorphism array-based copy-number variant (CNV) analyses.

RESULTS: Three patients had MECP2 mutations initially missed by clinical testing. Of the remaining 19, 17 (89.5\%) had 29 other likely pathogenic intragenic mutations and/or CNVs (10 patients had 2 or more). Interestingly, 13 patients had mutations in a gene/region previously reported in other neurodevelopmental disorders (NDDs), thereby providing a potential diagnostic yield of 68.4\%. These mutations were significantly enriched in chromatin regulators (corrected P = 0.0068) and moderately enriched in postsynaptic cell membrane molecules (corrected P = 0.076), implicating glutamate receptor signaling.

CONCLUSION: The genetic etiology of RTT without MECP2, CDKL5, and FOXG1 mutations is heterogeneous, overlaps with other NDDs, and complicated by a high mutation burden. Dysregulation of chromatin structure and abnormal excitatory synaptic signaling may form two common pathological bases of RTT.Genet Med 19 1, 13-19.

}, keywords = {Adolescent, Adult, Child, Child, Preschool, Chromatin, DNA Copy Number Variations, Female, Forkhead Transcription Factors, Humans, Infant, Male, Methyl-CpG-Binding Protein 2, Mutation, Nerve Tissue Proteins, Polymorphism, Single Nucleotide, Protein-Serine-Threonine Kinases, Rett Syndrome, Whole Exome Sequencing}, issn = {1530-0366}, doi = {10.1038/gim.2016.42}, author = {Sajan, Samin A and Jhangiani, Shalini N and Muzny, Donna M and Gibbs, Richard A and Lupski, James R and Glaze, Daniel G and Kaufmann, Walter E and Skinner, Steven A and Annese, Fran and Friez, Michael J and Lane, Jane and Percy, Alan K and Neul, Jeffrey L} } @article {368, title = {An exome sequencing study of Moebius syndrome including atypical cases reveals an individual with CFEOM3A and a mutation.}, journal = {Cold Spring Harb Mol Case Stud}, volume = {3}, year = {2017}, month = {2017 03}, pages = {a000984}, abstract = {

Moebius syndrome is characterized by congenital unilateral or bilateral facial and abducens nerve palsies (sixth and seventh cranial nerves) causing facial weakness, feeding difficulties, and restricted ocular movements. Abnormalities of the chest wall such as Poland anomaly and variable limb defects are frequently associated with this syndrome. Most cases are isolated; however, rare families with autosomal dominant transmission with incomplete penetrance and variable expressivity have been described. The genetic basis of this condition remains unknown. In a cohort study of nine individuals suspected to have Moebius syndrome (six typical, three atypical), we performed whole-exome sequencing to try to identify a commonly mutated gene. Although no such gene was identified and we did not find mutations in and , we found a de novo heterozygous mutation, p.E410K, in the gene encoding tubulin beta 3 class III (), in an individual with atypical Moebius syndrome. This individual was diagnosed with near-complete ophthalmoplegia, agenesis of the corpus callosum, and absence of the septum pellucidum. No substantial limb abnormalities were noted. Mutations in have been associated with complex cortical dysplasia and other brain malformations and congenital fibrosis of extraocular muscles type 3A (CFEOM3A). Our report highlights the overlap of genetic etiology and clinical differences between CFEOM and Moebius syndrome and describes our approach to identifying candidate genes for typical and atypical Moebius syndrome.

}, keywords = {Child, Child, Preschool, Cohort Studies, Exome, Eye Diseases, Hereditary, Facial Paralysis, Female, Humans, Infant, Male, Malformations of Cortical Development, Mobius Syndrome, Muscular Diseases, Mutation, Ocular Motility Disorders, Ophthalmoplegia, Orbital Diseases, Pedigree, Tubulin, Whole Exome Sequencing}, issn = {2373-2873}, doi = {10.1101/mcs.a000984}, author = {Patel, Ronak M and Liu, David and Gonzaga-Jauregui, Claudia and Jhangiani, Shalini and Lu, James T and Sutton, V Reid and Fernbach, Susan D and Azamian, Mahshid and White, Lisa and Edmond, Jane C and Paysse, Evelyn A and Belmont, John W and Muzny, Donna and Lupski, James R and Gibbs, Richard A and Lewis, Richard Alan and Lee, Brendan H and Lalani, Seema R and Campeau, Philippe M} } @article {39, title = {Exome sequencing in mostly consanguineous Arab families with neurologic disease provides a high potential molecular diagnosis rate.}, journal = {BMC Med Genomics}, volume = {9}, year = {2016}, month = {2016 Jul 19}, pages = {42}, abstract = {

BACKGROUND: Neurodevelopment is orchestrated by a wide range of genes, and the genetic causes of neurodevelopmental disorders are thus heterogeneous. We applied whole exome sequencing (WES) for molecular diagnosis and in silico analysis to identify novel disease gene candidates in a cohort from Saudi Arabia with primarily Mendelian neurologic diseases.

METHODS: We performed WES in 31 mostly consanguineous Arab families and analyzed both single nucleotide and copy number variants (CNVs) from WES data. Interaction/expression network and pathway analyses, as well as paralog studies were utilized to investigate potential pathogenicity and disease association of novel candidate genes. Additional cases for candidate genes were identified through the clinical WES database at Baylor Miraca Genetics Laboratories and GeneMatcher.

RESULTS: We found known pathogenic or novel variants in known disease genes with phenotypic expansion in 6 families, disease-associated CNVs in 2 families, and 12 novel disease gene candidates in 11 families, including KIF5B, GRM7, FOXP4, MLLT1, and KDM2B. Overall, a potential molecular diagnosis was provided by variants in known disease genes in 17 families (54.8~\%) and by novel candidate disease genes in an additional 11 families, making the potential molecular diagnostic rate ~90~\%.

CONCLUSIONS: Molecular diagnostic rate from WES is improved by exome-predicted CNVs. Novel candidate disease gene discovery is facilitated by paralog studies and through the use of informatics tools and available databases to identify additional evidence for pathogenicity.

TRIAL REGISTRATION: Not applicable.

}, keywords = {Arabs, Cohort Studies, Consanguinity, Data Mining, Databases, Genetic, DNA Copy Number Variations, Exome, Female, High-Throughput Nucleotide Sequencing, Humans, Male, Molecular Diagnostic Techniques, Nervous System Diseases, Pedigree, Phenotype, Polymorphism, Single Nucleotide, Sequence Analysis, DNA}, issn = {1755-8794}, doi = {10.1186/s12920-016-0208-3}, author = {Charng, Wu-Lin and Karaca, Ender and Coban Akdemir, Zeynep and Gambin, Tomasz and Atik, Mehmed M and Gu, Shen and Posey, Jennifer E and Jhangiani, Shalini N and Muzny, Donna M and Doddapaneni, Harsha and Hu, Jianhong and Boerwinkle, Eric and Gibbs, Richard A and Rosenfeld, Jill A and Cui, Hong and Xia, Fan and Manickam, Kandamurugu and Yang, Yaping and Faqeih, Eissa A and Al Asmari, Ali and Saleh, Mohammed A M and El-Hattab, Ayman W and Lupski, James R} } @article {135, title = {Exome Sequence Analysis Suggests that Genetic Burden Contributes to Phenotypic Variability and Complex Neuropathy.}, journal = {Cell Rep}, volume = {12}, year = {2015}, month = {2015 Aug 18}, pages = {1169-83}, abstract = {

Charcot-Marie-Tooth (CMT) disease is a clinically and genetically heterogeneous distal symmetric polyneuropathy. Whole-exome sequencing (WES) of 40 individuals from 37 unrelated families with CMT-like peripheral neuropathy refractory to molecular diagnosis identified apparent causal mutations in \~{} 45\% (17/37) of families. Three candidate disease genes are proposed, supported by a combination of genetic and in vivo studies. Aggregate analysis of mutation data revealed a significantly increased number of rare variants across 58 neuropathy-associated genes in subjects versus controls, confirmed in a second ethnically discrete neuropathy cohort, suggesting that mutation burden potentially contributes to phenotypic variability. Neuropathy genes shown to have highly penetrant Mendelizing variants (HPMVs) and implicated by burden in families were shown to interact genetically in a zebrafish assay exacerbating the phenotype established by the suppression of single genes. Our findings suggest that the combinatorial effect of rare variants contributes to disease burden and variable expressivity.

}, keywords = {Animals, Charcot-Marie-Tooth Disease, Exome, Female, Genetic Load, Genetic Variation, HSP40 Heat-Shock Proteins, Humans, Male, Mutation, Myelin P2 Protein, Pedigree, Penetrance, Peripheral Nervous System Diseases, Phenotype, Serine C-Palmitoyltransferase, Suppression, Genetic, Zebrafish}, issn = {2211-1247}, doi = {10.1016/j.celrep.2015.07.023}, author = {Gonzaga-Jauregui, Claudia and Harel, Tamar and Gambin, Tomasz and Kousi, Maria and Griffin, Laurie B and Francescatto, Ludmila and Ozes, Burcak and Karaca, Ender and Jhangiani, Shalini N and Bainbridge, Matthew N and Lawson, Kim S and Pehlivan, Davut and Okamoto, Yuji and Withers, Marjorie and Mancias, Pedro and Slavotinek, Anne and Reitnauer, Pamela J and Goksungur, Meryem T and Shy, Michael and Crawford, Thomas O and Koenig, Michel and Willer, Jason and Flores, Brittany N and Pediaditrakis, Igor and Us, Onder and Wiszniewski, Wojciech and Parman, Yesim and Antonellis, Anthony and Muzny, Donna M and Katsanis, Nicholas and Battaloglu, Esra and Boerwinkle, Eric and Gibbs, Richard A and Lupski, James R} } @article {181, title = {Exome sequencing identifies a homozygous C5orf42 variant in a Turkish kindred with oral-facial-digital syndrome type VI.}, journal = {Am J Med Genet A}, volume = {167A}, year = {2015}, month = {2015 Sep}, pages = {2132-7}, abstract = {

Oral-facial-digital syndrome type VI (OFDVI) is a rare ciliopathy in the spectrum of Joubert syndrome (JS) and distinguished from other oral-facial-digital syndromes by metacarpal abnormalities with central polydactyly and by a molar tooth sign on cranial MRI. Additional characteristic features include short stature, micrognathia, posteriorly rotated low-set ears, hypertelorism, epicanthal folds, broad nasal tip, tongue hamartoma, upper lip notch, intraoral frenula, cleft lip/palate, and renal anomalies. Recently, novel mutations in C5orf42 were identified in 9 out of 11 OFDVI families. In a subsequent study C5orf42 was found to be mutated in only 2 out of 17 OFDVI probands while 28 patients with a pure JS phenotype also had pathogenic mutations of C5orf42. We report on two affected cousins diagnosed with OFDVI who were born from first degree cousin marriages. Whole exome sequencing (WES) identified a homozygous predicted damaging missense mutation (c.4034A > G; p.Gln1345Arg) in the C5orf42 gene. Our data contribute to the evidence that C5orf42 is one of the causative genes for OFDVI.

}, keywords = {Abnormalities, Multiple, Cerebellar Diseases, Cerebellum, Child, Cleft Palate, Exome, Eye Abnormalities, Female, Genetic Predisposition to Disease, Hamartoma, Homozygote, Humans, Kidney Diseases, Cystic, Magnetic Resonance Imaging, Male, Membrane Proteins, Middle Aged, Mutation, Orofaciodigital Syndromes, Phenotype, Retina, Turkey}, issn = {1552-4833}, doi = {10.1002/ajmg.a.37092}, author = {Bayram, Yavuz and Aydin, Hatip and Gambin, Tomasz and Akdemir, Zeynep Coban and Atik, Mehmed M and Karaca, Ender and Karaman, Ali and Pehlivan, Davut and Jhangiani, Shalini N and Gibbs, Richard A and Lupski, James R} } @article {174, title = {Exome sequencing reveals homozygous TRIM2 mutation in a patient with early onset CMT and bilateral vocal cord paralysis.}, journal = {Hum Genet}, volume = {134}, year = {2015}, month = {2015 Jun}, pages = {671-3}, abstract = {

Charcot-Marie-Tooth disease is a heterogeneous group of inherited distal symmetric polyneuropathies associated with mutations in genes encoding components essential for normal functioning of the Schwann cell and axon. TRIM2, encoding a ligase that ubiquitinates the neurofilament light chain, was recently associated with early-onset neuropathy in a single patient. We report a TRIM2 homozygous missense mutation (c.2000A>C; p.D667A) in a patient with peripheral neuropathy and bilateral vocal cord paralysis, allowing for further delineation of the associated phenotypic spectrum.

}, keywords = {Adult, Charcot-Marie-Tooth Disease, Exome, Female, High-Throughput Nucleotide Sequencing, Homozygote, Humans, Infant, Newborn, Male, Mutation, Missense, Nuclear Proteins, Vocal Cord Paralysis}, issn = {1432-1203}, doi = {10.1007/s00439-015-1548-3}, author = {Pehlivan, Davut and Coban Akdemir, Zeynep and Karaca, Ender and Bayram, Yavuz and Jhangiani, Shalini and Yildiz, Edibe Pembegul and Muzny, Donna and Uluc, Kayihan and Gibbs, Richard A and Elcioglu, Nursel and Lupski, James R and Harel, Tamar} } @article {285, title = {Exonic duplication CNV of NDRG1 associated with autosomal-recessive HMSN-Lom/CMT4D.}, journal = {Genet Med}, volume = {16}, year = {2014}, month = {2014 May}, pages = {386-394}, abstract = {

PURPOSE: Copy-number variations as a mutational mechanism contribute significantly to human disease. Approximately one-half of the patients with Charcot-Marie-Tooth (CMT) disease have a 1.4 Mb duplication copy-number variation as the cause of their neuropathy. However, non-CMT1A neuropathy patients rarely have causative copy-number variations, and to date, autosomal-recessive disease has not been associated with copy-number variation as a mutational mechanism.

METHODS: We performed Agilent 8 {\texttimes} 60 K array comparative genomic hybridization on DNA from 12 recessive Turkish families with CMT disease. Additional molecular studies were conducted to detect breakpoint junctions and to evaluate gene expression levels in a family in which we detected an intragenic duplication copy-number variation.

RESULTS: We detected an ~6.25 kb homozygous intragenic duplication in NDRG1, a gene known to be causative for recessive HMSNL/CMT4D, in three individuals from a Turkish family with CMT neuropathy. Further studies showed that this intragenic copy-number variation resulted in a homozygous duplication of exons 6-8 that caused decreased mRNA expression of NDRG1.

CONCLUSION: Exon-focused high-resolution array comparative genomic hybridization enables the detection of copy-number variation carrier states in recessive genes, particularly small copy-number variations encompassing or disrupting single genes. In families for whom a molecular diagnosis has not been elucidated by conventional clinical assays, an assessment for copy-number variations in known CMT genes might be considered.

}, keywords = {Adult, Base Sequence, Cell Cycle Proteins, Charcot-Marie-Tooth Disease, Comparative Genomic Hybridization, DNA Copy Number Variations, Female, Gene Duplication, Gene Expression, Genes, Recessive, Humans, Intracellular Signaling Peptides and Proteins, Male, Mutation, Refsum Disease, Sequence Analysis, DNA, Turkey, Young Adult}, issn = {1530-0366}, doi = {10.1038/gim.2013.155}, author = {Okamoto, Yuji and Goksungur, Meryem Tuba and Pehlivan, Davut and Beck, Christine R and Gonzaga-Jauregui, Claudia and Muzny, Donna M and Atik, Mehmed M and Carvalho, Claudia M B and Matur, Zeliha and Bayraktar, Serife and Boone, Philip M and Akyuz, Kaya and Gibbs, Richard A and Battaloglu, Esra and Parman, Yesim and Lupski, James R} } @article {290, title = {Evidence for replicative mechanism in a CHD7 rearrangement in a patient with CHARGE syndrome.}, journal = {Am J Med Genet A}, volume = {161A}, year = {2013}, month = {2013 Dec}, pages = {3182-6}, abstract = {

Haploinsufficiency of CHD7 (OMIM$\#$ 608892) is known to cause CHARGE syndrome (OMIM$\#$ 214800). Molecular testing supports a definitive diagnosis in approximately 65-70\% of cases. Most CHD7 mutations arise de novo, and no mutations affecting exon-7 have been reported to date. We report on an 8-year-old girl diagnosed with CHARGE syndrome that was referred to our laboratory for comprehensive CHD7 gene screening. Genomic DNA from the subject with a suspected diagnosis of CHARGE was isolated from peripheral blood lymphocytes and comprehensive Sanger sequencing, along with deletion/duplication analysis of the CHD7 gene using multiplex ligation-dependent probe amplification (MLPA), was performed. MLPA analysis identified a reduced single probe signal for exon-7 of the CHD7 gene consistent with potential heterozygous deletion. Long-range PCR breakpoint analysis identified a complex genomic rearrangement (CGR) leading to the deletion of exon-7 and breakpoints consistent with a replicative mechanism such as fork stalling and template switching (FoSTeS) or microhomology-mediated break-induced replication (MMBIR). Taken together this represents the first evidence for a CHD7 intragenic CGR in a patient with CHARGE syndrome leading to what appears to be also the first report of a mutation specifically disrupting exon-7. Although likely rare, CGR may represent an overlooked mechanism in subjects with CHARGE syndrome that can be missed by current sequencing and dosage assays.

}, keywords = {Abnormalities, Multiple, CHARGE Syndrome, Child, DNA Helicases, DNA Replication, DNA-Binding Proteins, Exons, Female, Gene Deletion, Haploinsufficiency, Humans, Mutation}, issn = {1552-4833}, doi = {10.1002/ajmg.a.36178}, author = {Vatta, Matteo and Niu, Zhiyv and Lupski, James R and Putnam, Philip and Spoonamore, Katherine G and Fang, Ping and Eng, Christine M and Willis, Alecia S} } @article {298, title = {Exome sequencing resolves apparent incidental findings and reveals further complexity of SH3TC2 variant alleles causing Charcot-Marie-Tooth neuropathy.}, journal = {Genome Med}, volume = {5}, year = {2013}, month = {2013}, pages = {57}, abstract = {

BACKGROUND: The debate regarding the relative merits of whole genome sequencing (WGS) versus exome sequencing (ES) centers around comparative cost, average depth of coverage for each interrogated base, and their relative efficiency in the identification of medically actionable variants from the myriad of variants identified by each approach. Nevertheless, few genomes have been subjected to both WGS and ES, using multiple next generation sequencing platforms. In addition, no personal genome has been so extensively analyzed using DNA derived from peripheral blood as opposed to DNA from transformed cell lines that may either accumulate mutations during propagation or clonally expand mosaic variants during cell transformation and propagation.

METHODS: We investigated a genome that was studied previously by SOLiD chemistry using both ES and WGS, and now perform six independent ES assays (Illumina GAII (x2), Illumina HiSeq (x2), Life Technologies{\textquoteright} Personal Genome Machine (PGM) and Proton), and one additional WGS (Illumina HiSeq).

RESULTS: We compared the variants identified by the different methods and provide insights into the differences among variants identified between ES runs in the same technology platform and among different sequencing technologies. We resolved the true genotypes of medically actionable variants identified in the proband through orthogonal experimental approaches. Furthermore, ES identified an additional SH3TC2 variant (p.M1?) that likely contributes to the phenotype in the proband.

CONCLUSIONS: ES identified additional medically actionable variant calls and helped resolve ambiguous single nucleotide variants (SNV) documenting the power of increased depth of coverage of the captured targeted regions. Comparative analyses of WGS and ES reveal that pseudogenes and segmental duplications may explain some instances of apparent disease mutations in unaffected individuals.

}, issn = {1756-994X}, doi = {10.1186/gm461}, author = {Lupski, James R and Gonzaga-Jauregui, Claudia and Yang, Yaping and Bainbridge, Matthew N and Jhangiani, Shalini and Buhay, Christian J and Kovar, Christie L and Wang, Min and Hawes, Alicia C and Reid, Jeffrey G and Eng, Christine and Muzny, Donna M and Gibbs, Richard A} }