@article {774, title = {TBX6 missense variants expand the mutational spectrum in a non-Mendelian inheritance disease.}, journal = {Hum Mutat}, volume = {41}, year = {2020}, month = {2020 01}, pages = {182-195}, abstract = {

Congenital scoliosis (CS) is a birth defect with variable clinical and anatomical manifestations due to spinal malformation. The genetic etiology underlying about 10\% of CS cases in the Chinese population is compound inheritance by which the gene dosage is reduced below that of haploinsufficiency. In this genetic model, the trait manifests as a result of the combined effect of a rare variant and common pathogenic variant allele at a locus. From exome sequencing (ES) data of 523 patients in Asia and two patients in Texas, we identified six TBX6 gene-disruptive variants from 11 unrelated CS patients via ES and in vitro functional testing. The in trans mild hypomorphic allele was identified in 10 of the 11 subjects; as anticipated these 10 shared a similar spinal deformity of hemivertebrae. The remaining case has a homozygous variant in TBX6 (c.418C>T) and presents a more severe spinal deformity phenotype. We found decreased transcriptional activity and abnormal cellular localization as the molecular mechanisms for TBX6 missense loss-of-function alleles. Expanding the mutational spectrum of TBX6 pathogenic alleles enabled an increased molecular diagnostic detection rate, provided further evidence for the gene dosage-dependent genetic model underlying CS, and refined clinical classification.

}, keywords = {Alleles, Cell Line, Female, Gene Expression, Genes, Reporter, Genetic Association Studies, Genetic Predisposition to Disease, Genotype, Haplotypes, Humans, Inheritance Patterns, Male, Models, Molecular, Molecular Diagnostic Techniques, Mutation, Missense, Phenotype, Protein Conformation, Radiography, Sequence Analysis, DNA, Spine, Structure-Activity Relationship, T-Box Domain Proteins, Whole Exome Sequencing}, issn = {1098-1004}, doi = {10.1002/humu.23907}, author = {Chen, Weisheng and Lin, Jiachen and Wang, Lianlei and Li, Xiaoxin and Zhao, Sen and Liu, Jiaqi and Akdemir, Zeynep C and Zhao, Yanxue and Du, Renqian and Ye, Yongyu and Song, Xiaofei and Zhang, Yuanqiang and Yan, Zihui and Yang, Xinzhuang and Lin, Mao and Shen, Jianxiong and Wang, Shengru and Gao, Na and Yang, Ying and Liu, Ying and Li, Wenli and Liu, Jia and Zhang, Na and Yang, Xu and Xu, Yuan and Zhang, Jianguo and Delgado, Mauricio R and Posey, Jennifer E and Qiu, Guixing and Rios, Jonathan J and Liu, Pengfei and Wise, Carol A and Zhang, Feng and Wu, Zhihong and Lupski, James R and Wu, Nan} } @article {629, title = {A novel pathogenic variant in a family with paroxysmal kinesigenic dyskinesia and benign familial infantile seizures.}, journal = {Cold Spring Harb Mol Case Stud}, volume = {4}, year = {2018}, month = {2018 02}, abstract = {

Paroxysmal kinesigenic dyskinesia (PKD) is a rare neurological disorder characterized by recurrent attacks of dyskinetic movements without alteration of consciousness that are often triggered by the initiation of voluntary movements. Whole-exome sequencing has revealed a cluster of pathogenic variants in (proline-rich transmembrane protein), a gene with a function in synaptic regulation that remains poorly understood. Here, we report the discovery of a novel pathogenic variant inherited in an autosomal dominant pattern in a family with PKD and benign familial infantile seizures (BFIS). After targeted Sanger sequencing did not identify the presence of previously described pathogenic variants, we carried out whole-exome sequencing in the proband and her affected paternal grandfather. This led to the discovery of a novel variant, NM_001256442:exon3:c.C959T/NP_660282.2:p.A320V, altering an evolutionarily conserved alanine at the amino acid position 320 located in the M2 transmembrane region. Sanger sequencing further confirmed the presence of this variant in four affected family members (paternal grandfather, father, brother, and proband) and its absence in two unaffected ones (paternal grandmother and mother). This newly found variant further reinforces the importance of in PKD, BFIS, and possibly other movement disorders. Future functional studies using animal models and human pluripotent stem cell models will provide new insights into the role of and the significance of this variant in regulating neural development and/or function.

}, keywords = {Amino Acid Sequence, Base Sequence, Child, Chromosome Segregation, Conserved Sequence, Dystonia, Epilepsy, Benign Neonatal, Evolution, Molecular, Family, Female, Humans, Infant, Inheritance Patterns, Male, Membrane Proteins, Mutation, Nerve Tissue Proteins, Pedigree}, issn = {2373-2873}, doi = {10.1101/mcs.a002287}, author = {Lu, Jacqueline G and Bishop, Juliet and Cheyette, Sarah and Zhulin, Igor B and Guo, Su and Sobreira, Nara and Brenner, Steven E} } @article {537, title = {Disruptions in asymmetric centrosome inheritance and WDR62-Aurora kinase B interactions in primary microcephaly.}, journal = {Sci Rep}, volume = {7}, year = {2017}, month = {2017 03 08}, pages = {43708}, abstract = {

Recessive mutations in WD repeat domain 62 (WDR62) cause microcephaly and a wide spectrum of severe brain malformations. Disruption of the mouse ortholog results in microcephaly underlain by reduced proliferation of neocortical progenitors during late neurogenesis, abnormalities in asymmetric centrosome inheritance leading to neuronal migration delays, and altered neuronal differentiation. Spindle pole localization of WDR62 and mitotic progression are defective in patient-derived fibroblasts, which, similar to mouse neocortical progenitors, transiently arrest at prometaphase. Expression of WDR62 is closely correlated with components of the chromosome passenger complex (CPC), a key regulator of mitosis. Wild type WDR62, but not disease-associated mutant forms, interacts with the CPC core enzyme Aurora kinase B and staining of CPC components at centromeres is altered in patient-derived fibroblasts. Our findings demonstrate critical and diverse functions of WDR62 in neocortical development and provide insight into the mechanisms by which its disruption leads to a plethora of structural abnormalities.

}, keywords = {Animals, Aurora Kinase B, Brain, Cell Cycle, Cell Differentiation, Cell Proliferation, Centrosome, Consanguinity, Disease Models, Animal, Epistasis, Genetic, Fluorescent Antibody Technique, Gene Expression, Humans, Inheritance Patterns, Male, Mice, Mice, Knockout, Microcephaly, Mutation, Nerve Tissue Proteins, Neural Stem Cells, Pedigree, Whole Genome Sequencing}, issn = {2045-2322}, doi = {10.1038/srep43708}, author = {Sgourdou, Paraskevi and Mishra-Gorur, Ketu and Saotome, Ichiko and Henagariu, Octavian and Tuysuz, Beyhan and Campos, Cynthia and Ishigame, Keiko and Giannikou, Krinio and Quon, Jennifer L and {\v S}estan, Nenad and {\c C}a{\u g}layan, Ahmet O and G{\"u}nel, Murat and Louvi, Angeliki} } @article {372, title = {Homozygous and hemizygous CNV detection from exome sequencing data in a Mendelian disease cohort.}, journal = {Nucleic Acids Res}, volume = {45}, year = {2017}, month = {2017 02 28}, pages = {1633-1648}, abstract = {

We developed an algorithm, HMZDelFinder, that uses whole exome sequencing (WES) data to identify rare and intragenic homozygous and hemizygous (HMZ) deletions that may represent complete loss-of-function of the indicated gene. HMZDelFinder was applied to 4866 samples in the Baylor-Hopkins Center for Mendelian Genomics (BHCMG) cohort and detected 773 HMZ deletion calls (567 homozygous or 206 hemizygous) with an estimated sensitivity of 86.5\% (82\% for single-exonic and 88\% for multi-exonic calls) and precision of 78\% (53\% single-exonic and 96\% for multi-exonic calls). Out of 773 HMZDelFinder-detected deletion calls, 82 were subjected to array comparative genomic hybridization (aCGH) and/or breakpoint PCR and 64 were confirmed. These include 18 single-exon deletions out of which 8 were exclusively detected by HMZDelFinder and not by any of seven other CNV detection tools examined. Further investigation of the 64 validated deletion calls revealed at least 15 pathogenic HMZ deletions. Of those, 7 accounted for 17-50\% of pathogenic CNVs in different disease cohorts where 7.1-11\% of the molecular diagnosis solved rate was attributed to CNVs. In summary, we present an algorithm to detect rare, intragenic, single-exon deletion CNVs using WES data; this tool can be useful for disease gene discovery efforts and clinical WES analyses.

}, keywords = {Algorithms, Alternative Splicing, Cohort Studies, Computational Biology, Consanguinity, Datasets as Topic, DNA Copy Number Variations, Exome, Genetic Diseases, Inborn, Hemizygote, High-Throughput Nucleotide Sequencing, Homozygote, Humans, Inheritance Patterns, Models, Genetic, Pedigree, Reproducibility of Results, Sequence Deletion, Workflow}, issn = {1362-4962}, doi = {10.1093/nar/gkw1237}, author = {Gambin, Tomasz and Akdemir, Zeynep C and Yuan, Bo and Gu, Shen and Chiang, Theodore and Carvalho, Claudia M B and Shaw, Chad and Jhangiani, Shalini and Boone, Philip M and Eldomery, Mohammad K and Karaca, Ender and Bayram, Yavuz and Stray-Pedersen, Asbj{\o}rg and Muzny, Donna and Charng, Wu-Lin and Bahrambeigi, Vahid and Belmont, John W and Boerwinkle, Eric and Beaudet, Arthur L and Gibbs, Richard A and Lupski, James R} } @article {425, title = {Whole exome sequencing in 342 congenital cardiac left sided lesion cases reveals extensive genetic heterogeneity and complex inheritance patterns.}, journal = {Genome Med}, volume = {9}, year = {2017}, month = {2017 10 31}, pages = {95}, abstract = {

BACKGROUND: Left-sided lesions (LSLs) account for an important fraction of severe congenital cardiovascular malformations (CVMs). The genetic contributions to LSLs are complex, and the mutations that cause these malformations span several diverse biological signaling pathways: TGFB, NOTCH, SHH, and more. Here, we use whole exome sequence data generated in 342 LSL cases to identify likely damaging variants in putative candidate CVM genes.

METHODS: Using a series of bioinformatics filters, we focused on genes harboring population-rare, putative loss-of-function (LOF), and predicted damaging variants in 1760 CVM candidate genes constructed a priori from the literature and model organism databases. Gene variants that were not observed in a comparably sequenced control dataset of 5492 samples without severe CVM were then subjected to targeted validation in cases and parents. Whole exome sequencing data from 4593 individuals referred for clinical sequencing were used to bolster evidence for the role of candidate genes in CVMs and LSLs.

RESULTS: Our analyses revealed 28 candidate variants in 27 genes, including 17 genes not previously associated with a human CVM disorder, and revealed diverse patterns of inheritance among LOF carriers, including 9 confirmed de novo variants in both novel and newly described human CVM candidate genes (ACVR1, JARID2, NR2F2, PLRG1, SMURF1) as well as established syndromic CVM genes (KMT2D, NF1, TBX20, ZEB2). We also identified two genes (DNAH5, OFD1) with evidence of recessive and hemizygous inheritance patterns, respectively. Within our clinical cohort, we also observed heterozygous LOF variants in JARID2 and SMAD1 in individuals with cardiac phenotypes, and collectively, carriers of LOF variants in our candidate genes had a four times higher odds of having CVM (odds ratio = 4.0, 95\% confidence interval 2.5-6.5).

CONCLUSIONS: Our analytical strategy highlights the utility of bioinformatic resources, including human disease records and model organism phenotyping, in novel gene discovery for rare human disease. The results underscore the extensive genetic heterogeneity underlying non-syndromic LSLs, and posit potential novel candidate genes and complex modes of inheritance in this important group of birth defects.

}, keywords = {Female, Genetic Heterogeneity, Heart Defects, Congenital, Humans, Inheritance Patterns, Male, Whole Exome Sequencing}, issn = {1756-994X}, doi = {10.1186/s13073-017-0482-5}, author = {Li, Alexander H and Hanchard, Neil A and Furthner, Dieter and Fernbach, Susan and Azamian, Mahshid and Nicosia, Annarita and Rosenfeld, Jill and Muzny, Donna and D{\textquoteright}Alessandro, Lisa C A and Morris, Shaine and Jhangiani, Shalini and Parekh, Dhaval R and Franklin, Wayne J and Lewin, Mark and Towbin, Jeffrey A and Penny, Daniel J and Fraser, Charles D and Martin, James F and Eng, Christine and Lupski, James R and Gibbs, Richard A and Boerwinkle, Eric and Belmont, John W} } @article {108, title = {De Novo GMNN Mutations Cause Autosomal-Dominant Primordial Dwarfism Associated with Meier-Gorlin Syndrome.}, journal = {Am J Hum Genet}, volume = {97}, year = {2015}, month = {2015 Dec 03}, pages = {904-13}, abstract = {

Meier-Gorlin syndrome (MGS) is a genetically heterogeneous primordial dwarfism syndrome known to be caused by biallelic loss-of-function mutations in one of five genes encoding pre-replication complex proteins: ORC1, ORC4, ORC6, CDT1, and CDC6. Mutations in these genes cause disruption of the origin of DNA replication initiation. To date, only an autosomal-recessive inheritance pattern has been described in individuals with this disorder, with a molecular etiology established in about three-fourths of cases. Here, we report three subjects with MGS and de novo heterozygous mutations in the 5{\textquoteright} end of GMNN, encoding the DNA replication inhibitor geminin. We identified two truncating mutations in exon 2 (the 1(st) coding exon), c.16A>T (p.Lys6(*)) and c.35_38delTCAA (p.Ile12Lysfs(*)4), and one missense mutation, c.50A>G (p.Lys17Arg), affecting the second-to-last nucleotide of exon 2 and possibly RNA splicing. Geminin is present during the S, G2, and M phases of the cell cycle and is degraded during the metaphase-anaphase transition by the anaphase-promoting complex (APC), which recognizes the destruction box sequence near the 5{\textquoteright} end of the geminin protein. All three GMNN mutations identified alter sites 5{\textquoteright} to residue Met28 of the protein, which is located within the destruction box. We present data supporting a gain-of-function mechanism, in which the GMNN mutations result in proteins lacking the destruction box and hence increased protein stability and prolonged inhibition of replication leading to autosomal-dominant MGS.

}, keywords = {Adolescent, Amino Acid Sequence, Base Sequence, Cell Cycle, Child, Preschool, Congenital Microtia, Dwarfism, Exons, Female, Geminin, Gene Expression, Genes, Dominant, Growth Disorders, Heterozygote, High-Throughput Nucleotide Sequencing, Humans, Inheritance Patterns, Male, Micrognathism, Molecular Sequence Data, Mutation, Patella, Pedigree, Protein Stability, Proteolysis, RNA Splicing, Sequence Alignment}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2015.11.006}, author = {Burrage, Lindsay C and Charng, Wu-Lin and Eldomery, Mohammad K and Willer, Jason R and Davis, Erica E and Lugtenberg, Dorien and Zhu, Wenmiao and Leduc, Magalie S and Akdemir, Zeynep C and Azamian, Mahshid and Zapata, Gladys and Hernandez, Patricia P and Schoots, Jeroen and de Munnik, Sonja A and Roepman, Ronald and Pearring, Jillian N and Jhangiani, Shalini and Katsanis, Nicholas and Vissers, Lisenka E L M and Brunner, Han G and Beaudet, Arthur L and Rosenfeld, Jill A and Muzny, Donna M and Gibbs, Richard A and Eng, Christine M and Xia, Fan and Lalani, Seema R and Lupski, James R and Bongers, Ernie M H F and Yang, Yaping} } @article {109, title = {Mutations in Either TUBB or MAPRE2 Cause Circumferential Skin Creases Kunze Type.}, journal = {Am J Hum Genet}, volume = {97}, year = {2015}, month = {2015 Dec 03}, pages = {790-800}, abstract = {

Circumferential skin creases Kunze type (CSC-KT) is a specific congenital entity with an unknown genetic cause. The disease phenotype comprises characteristic circumferential skin creases accompanied by intellectual disability, a cleft palate, short stature, and dysmorphic features. Here, we report that mutations in either MAPRE2 or TUBB underlie the genetic origin of this syndrome. MAPRE2 encodes a member of the microtubule end-binding family of proteins that bind to the guanosine triphosphate cap at growing microtubule plus ends, and TUBB encodes a β-tubulin isotype that is expressed abundantly in the developing brain. Functional analyses of the TUBB mutants show multiple defects in the chaperone-dependent tubulin heterodimer folding and assembly pathway that leads to a compromised yield of native heterodimers. The TUBB mutations also have an impact on microtubule dynamics. For MAPRE2, we show that the mutations result in enhanced MAPRE2 binding to microtubules, implying an increased dwell time at microtubule plus ends. Further, in vivo analysis of MAPRE2 mutations in a zebrafish model of craniofacial development shows that the variants most likely perturb the patterning of branchial arches, either through excessive activity (under a recessive paradigm) or through haploinsufficiency (dominant de novo paradigm). Taken together, our data add CSC-KT to the growing list of tubulinopathies and highlight how multiple inheritance paradigms can affect dosage-sensitive biological systems so as to result in the same clinical defect.

}, keywords = {Adolescent, Animals, Brain, Child, Cutis Laxa, Female, Gene Dosage, Gene Expression Regulation, Developmental, Genes, Recessive, Hamartoma, Haploinsufficiency, Humans, Infant, Inheritance Patterns, Male, Microtubule-Associated Proteins, Microtubules, Mutation, Protein Folding, Protein Multimerization, Skin, Skin Abnormalities, Tubulin, Young Adult, Zebrafish}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2015.10.014}, author = {Isrie, Mala and Breuss, Martin and Tian, Guoling and Hansen, Andi Harley and Cristofoli, Francesca and Morandell, Jasmin and Kupchinsky, Zachari A and Sifrim, Alejandro and Rodriguez-Rodriguez, Celia Maria and Dapena, Elena Porta and Doonanco, Kurston and Leonard, Norma and Tinsa, Faten and Moortgat, St{\'e}phanie and Ulucan, Hakan and Koparir, Erkan and Karaca, Ender and Katsanis, Nicholas and Marton, Valeria and Vermeesch, Joris Robert and Davis, Erica E and Cowan, Nicholas J and Keays, David Anthony and Van Esch, Hilde} } @article {244, title = {Cytogenomic delineation and clinical follow-up of two siblings with an 8.5 Mb 6q24.2-q25.2 deletion inherited from a paternal insertion.}, journal = {Am J Med Genet A}, volume = {164A}, year = {2014}, month = {2014 Sep}, pages = {2378-84}, abstract = {

The chromosomal segment 6q24-q25 comprises a contiguous gene microdeletion syndrome characterized by intrauterine growth retardation, growth delay, intellectual disability, cardiac anomalies, and a dysmorphic facial phenotype. We describe here a 10-year follow-up with detailed clinical, neuropsychological, and cytomolecular data of two siblings, male and female, who presented with developmental delay, microcephaly, short stature, characteristic facial dysmorphisms, multiple organ anomalies, and intellectual disability. Microarray analysis showed an 8.5 Mb 6q24.2-q25.2 interstitial deletion. Fluorescence in situ hybridization analyses confirmed the deletions and identified an insertion of 6q into 8q13 in their father, resulting in a high recurrence risk. This is the first report in sibs with distinct neuropsychological involvement, one of them with stenosis of the descending branch of the aorta.

}, keywords = {Adolescent, Base Pairing, Child, Child, Preschool, Chromosome Deletion, Chromosomes, Human, Pair 6, Cytogenetic Analysis, Fathers, Female, Follow-Up Studies, Humans, Infant, Newborn, Inheritance Patterns, Male, Mutagenesis, Insertional, Siblings}, issn = {1552-4833}, doi = {10.1002/ajmg.a.36631}, author = {Meloni, Vera Ayres and Guilherme, Roberta Santos and Oliveira, Mariana Moyses and Migliavacca, Michele and Takeno, Sylvia Satomi and Sobreira, Nara Lygia Macena and de Fatima Faria Soares, Maria and de Mello, Claudia Berlim and Melaragno, Maria Isabel} } @article {220, title = {A drosophila genetic resource of mutants to study mechanisms underlying human genetic diseases.}, journal = {Cell}, volume = {159}, year = {2014}, month = {2014 Sep 25}, pages = {200-214}, abstract = {

Invertebrate model systems are powerful tools for studying human disease owing to their genetic tractability and ease of screening. We conducted a mosaic genetic screen of lethal mutations on the Drosophila X chromosome to identify genes required for the development, function, and maintenance of the nervous system. We identified 165 genes, most of whose function has not been studied in vivo. In parallel, we investigated rare variant alleles in 1,929 human exomes from families with unsolved Mendelian disease. Genes that are essential in flies and have multiple human homologs were found to be likely to be associated with human diseases. Merging the human data sets with the fly genes allowed us to identify disease-associated mutations in six families and to provide insights into microcephaly associated with brain dysgenesis. This bidirectional synergism between fly genetics and human genomics facilitates the functional annotation of evolutionarily conserved genes involved in human health.

}, keywords = {Animals, Disease, Disease Models, Animal, Drosophila melanogaster, Genetic Testing, Humans, Inheritance Patterns, RNA Interference, X Chromosome}, issn = {1097-4172}, doi = {10.1016/j.cell.2014.09.002}, author = {Yamamoto, Shinya and Jaiswal, Manish and Charng, Wu-Lin and Gambin, Tomasz and Karaca, Ender and Mirzaa, Ghayda and Wiszniewski, Wojciech and Sandoval, Hector and Haelterman, Nele A and Xiong, Bo and Zhang, Ke and Bayat, Vafa and David, Gabriela and Li, Tongchao and Chen, Kuchuan and Gala, Upasana and Harel, Tamar and Pehlivan, Davut and Penney, Samantha and Vissers, Lisenka E L M and de Ligt, Joep and Jhangiani, Shalini N and Xie, Yajing and Tsang, Stephen H and Parman, Yesim and Sivaci, Merve and Battaloglu, Esra and Muzny, Donna and Wan, Ying-Wooi and Liu, Zhandong and Lin-Moore, Alexander T and Clark, Robin D and Curry, Cynthia J and Link, Nichole and Schulze, Karen L and Boerwinkle, Eric and Dobyns, William B and Allikmets, Rando and Gibbs, Richard A and Chen, Rui and Lupski, James R and Wangler, Michael F and Bellen, Hugo J} } @article {222, title = {Parent of origin, mosaicism, and recurrence risk: probabilistic modeling explains the broken symmetry of transmission genetics.}, journal = {Am J Hum Genet}, volume = {95}, year = {2014}, month = {2014 Oct 02}, pages = {345-59}, abstract = {

Most new mutations are observed to arise in fathers, and increasing paternal age positively correlates with the risk of new variants. Interestingly, new mutations in X-linked recessive disease show elevated familial recurrence rates. In male offspring, these mutations must be inherited from mothers. We previously developed a simulation model to consider parental mosaicism as a source of transmitted mutations. In this paper, we extend and formalize the model to provide analytical results and flexible formulas. The results implicate parent of origin and parental mosaicism as central variables in recurrence risk. Consistent with empirical data, our model predicts that more transmitted mutations arise in fathers and that this tendency increases as fathers age. Notably, the lack of expansion later in the male germline determines relatively lower variance in the proportion of mutants, which decreases with paternal age. Subsequently, observation of a transmitted mutation has less impact on the expected risk for future offspring. Conversely, for the female germline, which arrests after clonal expansion in early development, variance in the mutant proportion is higher, and observation of a transmitted mutation dramatically increases the expected risk of recurrence in another pregnancy. Parental somatic mosaicism considerably elevates risk for both parents. These findings have important implications for genetic counseling and for understanding patterns of recurrence in transmission genetics. We provide a convenient online tool and source code implementing our analytical results. These tools permit varying the underlying parameters that influence recurrence risk and could be useful for analyzing risk in diverse family structures.

}, keywords = {Adult, Aged, Aged, 80 and over, Chromosome Aberrations, DNA Copy Number Variations, Fathers, Female, Gametogenesis, Genetic Diseases, Inborn, Genomics, Germ Cells, Germ-Line Mutation, Humans, Inheritance Patterns, Male, Middle Aged, Models, Theoretical, Mosaicism, Mothers, Pregnancy, Recurrence, Risk Factors, Young Adult}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2014.08.010}, author = {Campbell, Ian M and Stewart, Jonathan R and James, Regis A and Lupski, James R and Stankiewicz, Pawe{\l} and Olofsson, Peter and Shaw, Chad A} } @article {323, title = {Incidental copy-number variants identified by routine genome testing in a clinical population.}, journal = {Genet Med}, volume = {15}, year = {2013}, month = {2013 Jan}, pages = {45-54}, abstract = {

PURPOSE: Mutational load of susceptibility variants has not been studied on a genomic scale in a clinical population, nor has the potential to identify these mutations as incidental findings during clinical testing been systematically ascertained.

METHODS: Array comparative genomic hybridization, a method for genome-wide detection of DNA copy-number variants, was performed clinically on DNA from 9,005 individuals. Copy-number variants encompassing or disrupting single genes were identified and analyzed for their potential to confer predisposition to dominant, adult-onset disease. Multigene copy-number variants affecting dominant, adult-onset cancer syndrome genes were also assessed.

RESULTS: In our cohort, 83 single-gene copy-number variants affected 40 unique genes associated with dominant, adult-onset disorders and unrelated to the patients{\textquoteright} referring diagnoses (i.e., incidental) were found. Fourteen of these copy-number variants are likely disease-predisposing, 25 are likely benign, and 44 are of unknown clinical consequence. When incidental copy-number variants spanning up to 20 genes were considered, 27 copy-number variants affected 17 unique genes associated with dominant, adult-onset cancer predisposition.

CONCLUSION: Copy-number variants potentially conferring susceptibility to adult-onset disease can be identified as incidental findings during routine genome-wide testing. Some of these mutations may be medically actionable, enabling disease surveillance or prevention; however, most incidentally observed single-gene copy-number variants are currently of unclear significance to the patient.

}, keywords = {Age of Onset, Base Sequence, Chromosome Mapping, Comparative Genomic Hybridization, DNA Copy Number Variations, Female, Gene Order, Genetic Predisposition to Disease, Humans, Inheritance Patterns, Male, Reproducibility of Results}, issn = {1530-0366}, doi = {10.1038/gim.2012.95}, author = {Boone, Philip M and Soens, Zachry T and Campbell, Ian M and Stankiewicz, Pawel and Cheung, Sau Wai and Patel, Ankita and Beaudet, Arthur L and Plon, Sharon E and Shaw, Chad A and McGuire, Amy L and Lupski, James R} }