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Bayer, D. K. et al. Vaccine-associated varicella and rubella infections in severe combined immunodeficiency with isolated CD4 lymphocytopenia and mutations in IL7R detected by tandem whole exome sequencing and chromosomal microarray. Clin Exp Immunol 178, 459-69 (2014).
Bekheirnia, M. Reza et al. Whole-exome sequencing in the molecular diagnosis of individuals with congenital anomalies of the kidney and urinary tract and identification of a new causative gene. Genet Med 19, 412-420 (2017).
Boone, P. M. et al. Incidental copy-number variants identified by routine genome testing in a clinical population. Genet Med 15, 45-54 (2013).
Boone, P. M. et al. Deletions of recessive disease genes: CNV contribution to carrier states and disease-causing alleles. Genome Res 23, 1383-94 (2013).
Boone, P. M. et al. The Alu-rich genomic architecture of SPAST predisposes to diverse and functionally distinct disease-associated CNV alleles. Am J Hum Genet 95, 143-61 (2014).
Brasó-Vives, M. et al. Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta). PLoS Genet 16, e1008742 (2020).
Brownstein, C. A. et al. Overlapping 16p13.11 deletion and gain of copies variations associated with childhood onset psychosis include genes with mechanistic implications for autism associated pathways: Two case reports. Am J Med Genet A 170A, 1165-73 (2016).
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Çağlayan, A. O. et al. A patient with a novel homozygous missense mutation in FTO and concomitant nonsense mutation in CETP. J Hum Genet 61, 395-403 (2016).
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Cai, Y. et al. Copy Number Changes Identified Using Whole Exome Sequencing in Nonsyndromic Cleft Lip and Palate in a Honduran Population. Birth Defects Res 109, 1257-1267 (2017).
Campbell, I. M. et al. Parental somatic mosaicism is underrecognized and influences recurrence risk of genomic disorders. Am J Hum Genet 95, 173-82 (2014).
Campbell, I. M. et al. Parent of origin, mosaicism, and recurrence risk: probabilistic modeling explains the broken symmetry of transmission genetics. Am J Hum Genet 95, 345-59 (2014).
Carvalho, C. M. B. et al. Absence of heterozygosity due to template switching during replicative rearrangements. Am J Hum Genet 96, 555-64 (2015).
Carvalho, C. M. B. et al. Replicative mechanisms for CNV formation are error prone. Nat Genet 45, 1319-26 (2013).
Charng, W. - L. et al. Exome sequencing in mostly consanguineous Arab families with neurologic disease provides a high potential molecular diagnosis rate. BMC Med Genomics 9, 42 (2016).
Chen, L. et al. CNV instability associated with DNA replication dynamics: evidence for replicative mechanisms in CNV mutagenesis. Hum Mol Genet 24, 1574-83 (2015).
Chen, L. et al. Association of structural variation with cardiometabolic traits in Finns. Am J Hum Genet 108, 583-596 (2021).
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Eldomery, M. K. et al. Lessons learned from additional research analyses of unsolved clinical exome cases. Genome Med 9, 26 (2017).
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Gambin, T. et al. Identification of novel candidate disease genes from de novo exonic copy number variants. Genome Med 9, 83 (2017).
Gambin, T. et al. Homozygous and hemizygous CNV detection from exome sequencing data in a Mendelian disease cohort. Nucleic Acids Res 45, 1633-1648 (2017).
Glessner, J. T. et al. Increased frequency of de novo copy number variants in congenital heart disease by integrative analysis of single nucleotide polymorphism array and exome sequence data. Circ Res 115, 884-896 (2014).
Goh, G. et al. Recurrent activating mutation in PRKACA in cortisol-producing adrenal tumors. Nat Genet 46, 613-7 (2014).
Gu, S. et al. Mechanisms for the Generation of Two Quadruplications Associated with Split-Hand Malformation. Hum Mutat 37, 160-4 (2016).
Gu, S. et al. Alu-mediated diverse and complex pathogenic copy-number variants within human chromosome 17 at p13.3. Hum Mol Genet 24, 4061-77 (2015).
Guissart, C. et al. Dual Molecular Effects of Dominant RORA Mutations Cause Two Variants of Syndromic Intellectual Disability with Either Autism or Cerebellar Ataxia. Am J Hum Genet 102, 744-759 (2018).
Gunning, A. C. et al. Recurrent De Novo NAHR Reciprocal Duplications in the ATAD3 Gene Cluster Cause a Neurogenetic Trait with Perturbed Cholesterol and Mitochondrial Metabolism. Am J Hum Genet 106, 272-279 (2020).
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Harel, T. et al. Recurrent De Novo and Biallelic Variation of ATAD3A, Encoding a Mitochondrial Membrane Protein, Results in Distinct Neurological Syndromes. Am J Hum Genet 99, 831-845 (2016).
Hjeij, R. et al. ARMC4 mutations cause primary ciliary dyskinesia with randomization of left/right body asymmetry. Am J Hum Genet 93, 357-67 (2013).
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Karolak, J. A. et al. Complex Compound Inheritance of Lethal Lung Developmental Disorders Due to Disruption of the TBX-FGF Pathway. Am J Hum Genet 104, 213-228 (2019).
Küry, S. et al. De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder. Am J Hum Genet 100, 352-363 (2017).
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Lee, W. et al. Complex inheritance of ABCA4 disease: four mutations in a family with multiple macular phenotypes. Hum Genet 135, 9-19 (2016).
Lindstrand, A. et al. Copy-Number Variation Contributes to the Mutational Load of Bardet-Biedl Syndrome. Am J Hum Genet 99, 318-36 (2016).
Liu, P. et al. An Organismal CNV Mutator Phenotype Restricted to Early Human Development. Cell 168, 830-842.e7 (2017).
Liu, J. et al. The coexistence of copy number variations (CNVs) and single nucleotide polymorphisms (SNPs) at a locus can result in distorted calculations of the significance in associating SNPs to disease. Hum Genet 137, 553-567 (2018).
Liu, Q., Grochowski, C. M., Bi, W., Lupski, J. R. & Stankiewicz, P. Quantitative Assessment of Parental Somatic Mosaicism for Copy-Number Variant (CNV) Deletions. Curr Protoc Hum Genet 106, e99 (2020).
Lodish, M. B. et al. Germline PRKACA amplification causes variable phenotypes that may depend on the extent of the genomic defect: molecular mechanisms and clinical presentations. Eur J Endocrinol 172, 803-11 (2015).
Lupski, J. R. Cognitive phenotypes and genomic copy number variations. JAMA 313, 2029-30 (2015).
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Niestroj, L. - M. et al. Epilepsy subtype-specific copy number burden observed in a genome-wide study of 17 458 subjects. Brain 143, 2106-2118 (2020).
Nilsson, D. et al. Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in the Mechanism of Formation. Hum Mutat 38, 180-192 (2017).
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Okamoto, Y. et al. Exonic duplication CNV of NDRG1 associated with autosomal-recessive HMSN-Lom/CMT4D. Genet Med 16, 386-394 (2014).
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Pehlivan, D. et al. The role of combined SNV and CNV burden in patients with distal symmetric polyneuropathy. Genet Med 18, 443-51 (2016).
Peter, B. et al. Genetic Candidate Variants in Two Multigenerational Families with Childhood Apraxia of Speech. PLoS One 11, e0153864 (2016).
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Qi, H. et al. De novo variants in congenital diaphragmatic hernia identify MYRF as a new syndrome and reveal genetic overlaps with other developmental disorders. PLoS Genet 14, e1007822 (2018).
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Sadedin, S. P., Ellis, J. A., Masters, S. L. & Oshlack, A. Ximmer: a system for improving accuracy and consistency of CNV calling from exome data. Gigascience 7, (2018).
Saettini, F. et al. Absent B cells, agammaglobulinemia, and hypertrophic cardiomyopathy in folliculin-interacting protein 1 deficiency. Blood 137, 493-499 (2021).
Sajan, S. A. et al. Enrichment of mutations in chromatin regulators in people with Rett syndrome lacking mutations in MECP2. Genet Med 19, 13-19 (2017).
Shen, F. & Kidd, J. M. Rapid, Paralog-Sensitive CNV Analysis of 2457 Human Genomes Using QuicK-mer2. Genes (Basel) 11, (2020).
Song, X. et al. Predicting human genes susceptible to genomic instability associated with /-mediated rearrangements. Genome Res 28, 1228-1242 (2018).
Stray-Pedersen, A. et al. Primary immunodeficiency diseases: Genomic approaches delineate heterogeneous Mendelian disorders. J Allergy Clin Immunol 139, 232-245 (2017).
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Whitman, M. C. et al. Recurrent Rare Copy Number Variants Increase Risk for Esotropia. Invest Ophthalmol Vis Sci 61, 22 (2020).
Wiszniewski, W. et al. Comprehensive genomic analysis of patients with disorders of cerebral cortical development. Eur J Hum Genet 26, 1121-1131 (2018).

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