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A
Aldinger, K. A. et al. Mutations in LAMA1 cause cerebellar dysplasia and cysts with and without retinal dystrophy. Am J Hum Genet 95, 227-34 (2014).
Ansar, M. et al. A homozygous missense variant in type I keratin KRT25 causes autosomal recessive woolly hair. J Med Genet 52, 676-80 (2015).
Aylward, A. et al. Using Whole Exome Sequencing to Identify Candidate Genes With Rare Variants In Nonsyndromic Cleft Lip and Palate. Genet Epidemiol 40, 432-41 (2016).
B
Bachmann-Gagescu, R. et al. Joubert syndrome: a model for untangling recessive disorders with extreme genetic heterogeneity. J Med Genet 52, 514-22 (2015).
Bennett, J. T. et al. Mosaic Activating Mutations in FGFR1 Cause Encephalocraniocutaneous Lipomatosis. Am J Hum Genet 98, 579-587 (2016).
Bilguvar, K. et al. Recessive loss of function of the neuronal ubiquitin hydrolase UCHL1 leads to early-onset progressive neurodegeneration. Proc Natl Acad Sci U S A 110, 3489-94 (2013).
Bonora, E. et al. Mutations in RAD21 disrupt regulation of APOB in patients with chronic intestinal pseudo-obstruction. Gastroenterology 148, 771-782.e11 (2015).
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).
Boyden, L. M. et al. Dominant De Novo Mutations in GJA1 Cause Erythrokeratodermia Variabilis et Progressiva, without Features of Oculodentodigital Dysplasia. J Invest Dermatol 135, 1540-1547 (2015).
Brasó-Vives, M. et al. Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta). PLoS Genet 16, e1008742 (2020).
Braun, D. A. et al. Mutations in nuclear pore genes NUP93, NUP205 and XPO5 cause steroid-resistant nephrotic syndrome. Nat Genet 48, 457-65 (2016).
C
Caglayan, A. O. et al. Whole-exome sequencing identified a patient with TMCO1 defect syndrome and expands the phenotic spectrum. Clin Genet 84, 394-5 (2013).
Campeau, P. M. et al. The genetic basis of DOORS syndrome: an exome-sequencing study. Lancet Neurol 13, 44-58 (2014).
Carmody, D. et al. Continued lessons from the INS gene: an intronic mutation causing diabetes through a novel mechanism. J Med Genet 52, 612-6 (2015).
Carvalho, C. M. B. et al. Replicative mechanisms for CNV formation are error prone. Nat Genet 45, 1319-26 (2013).
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. Dosage changes of a segment at 17p13.1 lead to intellectual disability and microcephaly as a result of complex genetic interaction of multiple genes. Am J Hum Genet 95, 565-78 (2014).
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, W. et al. TBX6 missense variants expand the mutational spectrum in a non-Mendelian inheritance disease. Hum Mutat 41, 182-195 (2020).
Chen, S., Mattei, P., You, J., Sobreira, N. L. & Hinds, G. A. γ-Secretase Mutation in an African American Family With Hidradenitis Suppurativa. JAMA Dermatol 151, 668-70 (2015).
Cheung, Y. Him et al. A recurrent PDGFRB mutation causes familial infantile myofibromatosis. Am J Hum Genet 92, 996-1000 (2013).
Cheung, Y. Him, Wang, G., Leal, S. M. & Wang, S. A fast and noise-resilient approach to detect rare-variant associations with deep sequencing data for complex disorders. Genet Epidemiol 36, 675-85 (2012).
Collison, F. T. et al. Whole Exome Sequencing Identifies an Adult-Onset Case of Methylmalonic Aciduria and Homocystinuria Type C (cblC) with Non-Syndromic Bull's Eye Maculopathy. Ophthalmic Genet 36, 270-5 (2015).
E
Ebert, P. et al. Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science 372, (2021).
Eldomery, M. K. et al. Lessons learned from additional research analyses of unsolved clinical exome cases. Genome Med 9, 26 (2017).
English, A. C. et al. Assessing structural variation in a personal genome-towards a human reference diploid genome. BMC Genomics 16, 286 (2015).
F
Farlow, J. L. et al. Whole-Exome Sequencing in Familial Parkinson Disease. JAMA Neurol 73, 68-75 (2016).
Fieremans, N. et al. Identification of Intellectual Disability Genes in Female Patients with a Skewed X-Inactivation Pattern. Hum Mutat 37, 804-11 (2016).
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Goh, G. et al. Recurrent activating mutation in PRKACA in cortisol-producing adrenal tumors. Nat Genet 46, 613-7 (2014).
Green, R. C., Lupski, J. R. & Biesecker, L. G. Reporting genomic sequencing results to ordering clinicians: incidental, but not exceptional. JAMA 310, 365-6 (2013).
Gu, S. et al. Mechanisms for the Generation of Two Quadruplications Associated with Split-Hand Malformation. Hum Mutat 37, 160-4 (2016).
H
Hampton, O. A. et al. SVachra: a tool to identify genomic structural variation in mate pair sequencing data containing inward and outward facing reads. BMC Genomics 18, 691 (2017).
He, Z. et al. Rare-variant extensions of the transmission disequilibrium test: application to autism exome sequence data. Am J Hum Genet 94, 33-46 (2014).
J
Jamal, S. M. et al. Practices and policies of clinical exome sequencing providers: analysis and implications. Am J Med Genet A 161A, 935-50 (2013).
Jin, S. Chih et al. Mutations disrupting neuritogenesis genes confer risk for cerebral palsy. Nat Genet 52, 1046-1056 (2020).
Jurgens, J. et al. Novel COL2A1 variant (c.619G>A, p.Gly207Arg) manifesting as a phenotype similar to progressive pseudorheumatoid dysplasia and spondyloepiphyseal dysplasia, Stanescu type. Hum Mutat 36, 1004-8 (2015).
K
Kariminejad, A. et al. Kaufman oculo-cerebro-facial syndrome in a child with small and absent terminal phalanges and absent nails. J Hum Genet 62, 465-471 (2017).
Keller, R. B. et al. Monoallelic and biallelic CREB3L1 variant causes mild and severe osteogenesis imperfecta, respectively. Genet Med 20, 411-419 (2018).
Knowles, M. R. et al. Mutations in RSPH1 cause primary ciliary dyskinesia with a unique clinical and ciliary phenotype. Am J Respir Crit Care Med 189, 707-17 (2014).
Kornilov, S. A. et al. Genome-Wide Association and Exome Sequencing Study of Language Disorder in an Isolated Population. Pediatrics 137, (2016).
Kuehn, H. S. et al. Loss of B Cells in Patients with Heterozygous Mutations in IKAROS. N Engl J Med 374, 1032-1043 (2016).
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Lalani, S. R. et al. Mutations in PURA cause profound neonatal hypotonia, seizures, and encephalopathy in 5q31.3 microdeletion syndrome. Am J Hum Genet 95, 579-83 (2014).
Latif, Z. et al. Confirmation of the Role of DHX38 in the Etiology of Early-Onset Retinitis Pigmentosa. Invest Ophthalmol Vis Sci 59, 4552-4557 (2018).
Law, R. et al. Biallelic truncating mutations in FMN2, encoding the actin-regulatory protein Formin 2, cause nonsyndromic autosomal-recessive intellectual disability. Am J Hum Genet 95, 721-8 (2014).
Levinsohn, J. L. et al. Somatic HRAS p.G12S mutation causes woolly hair and epidermal nevi. J Invest Dermatol 134, 1149-1152 (2014).
Levinsohn, J. L. et al. Whole-exome sequencing reveals somatic mutations in HRAS and KRAS, which cause nevus sebaceus. J Invest Dermatol 133, 827-830 (2013).
Lim, Y. H. et al. Multilineage somatic activating mutations in HRAS and NRAS cause mosaic cutaneous and skeletal lesions, elevated FGF23 and hypophosphatemia. Hum Mol Genet 23, 397-407 (2014).
Liu, P. et al. Reanalysis of Clinical Exome Sequencing Data. N Engl J Med 380, 2478-2480 (2019).
Liu, D. J. & Leal, S. M. SEQCHIP: a powerful method to integrate sequence and genotype data for the detection of rare variant associations. Bioinformatics 28, 1745-51 (2012).
Lo, S. M. et al. Phenotype diversity in type 1 Gaucher disease: discovering the genetic basis of Gaucher disease/hematologic malignancy phenotype by individual genome analysis. Blood 119, 4731-40 (2012).

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