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A
Abel, H. J. et al. Mapping and characterization of structural variation in 17,795 human genomes. Nature 583, 83-89 (2020).
Alodaib, A. et al. Whole-exome sequencing identifies novel variants in PNPT1 causing oxidative phosphorylation defects and severe multisystem disease. Eur J Hum Genet 25, 79-84 (2016).
Aneichyk, T. et al. Dissecting the Causal Mechanism of X-Linked Dystonia-Parkinsonism by Integrating Genome and Transcriptome Assembly. Cell 172, 897-909.e21 (2018).
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
Bamshad, M. J. et al. The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions. Am J Med Genet A 158A, 1523-5 (2012).
Bergner, A. L. et al. Informed consent for exome sequencing research in families with genetic disease: the emerging issue of incidental findings. Am J Med Genet A 164A, 2745-52 (2014).
Brasó-Vives, M. et al. Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta). PLoS Genet 16, e1008742 (2020).
Burrage, L. C. et al. De Novo GMNN Mutations Cause Autosomal-Dominant Primordial Dwarfism Associated with Meier-Gorlin Syndrome. Am J Hum Genet 97, 904-13 (2015).
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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).
C
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).
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, D. - H. et al. Ataxia-Pancytopenia Syndrome Is Caused by Missense Mutations in SAMD9L. Am J Hum Genet 98, 1146-1158 (2016).
Chen, L. et al. Association of structural variation with cardiometabolic traits in Finns. Am J Hum Genet 108, 583-596 (2021).
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).
Chong, J. X. et al. De novo mutations in NALCN cause a syndrome characterized by congenital contractures of the limbs and face, hypotonia, and developmental delay. Am J Hum Genet 96, 462-73 (2015).
Chong, J. X. et al. Autosomal-Dominant Multiple Pterygium Syndrome Is Caused by Mutations in MYH3. Am J Hum Genet 96, 841-9 (2015).
Cummings, B. B. et al. Improving genetic diagnosis in Mendelian disease with transcriptome sequencing. Sci Transl Med 9, (2017).
E
Ebert, P. et al. Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science 372, (2021).
F
Fairfield, H. et al. Exome sequencing reveals pathogenic mutations in 91 strains of mice with Mendelian disorders. Genome Res 25, 948-57 (2015).
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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).
Gambin, T. et al. Low-level parental somatic mosaic SNVs in exomes from a large cohort of trios with diverse suspected Mendelian conditions. Genet Med 22, 1768-1776 (2020).
Grammatikopoulos, T. et al. Mutations in DCDC2 (doublecortin domain containing protein 2) in neonatal sclerosing cholangitis. J Hepatol 65, 1179-1187 (2016).
Gripp, K. W. et al. Truncating mutations in the last exon of NOTCH3 cause lateral meningocele syndrome. Am J Med Genet A 167A, 271-81 (2015).
Gulati, A., Dahl, N. & Tufro, A. Inherited glomerular diseases in the gilded age of genomic advancements. Pediatr Nephrol 35, 959-968 (2020).
Guo, D. - C. et al. Recurrent gain-of-function mutation in PRKG1 causes thoracic aortic aneurysms and acute aortic dissections. Am J Hum Genet 93, 398-404 (2013).
I
Issa, M. Y. et al. Molecular diagnosis in recessive pediatric neurogenetic disease can help reduce disease recurrence in families. BMC Med Genomics 13, 68 (2020).
J
Jin, S. Chih et al. Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands. Nat Genet 49, 1593-1601 (2017).
Jurgens, J. et al. Assessment of incidental findings in 232 whole-exome sequences from the Baylor-Hopkins Center for Mendelian Genomics. Genet Med 17, 782-8 (2015).
K
Karolak, J. A. et al. Variants in SKP1, PROB1, and IL17B genes at keratoconus 5q31.1-q35.3 susceptibility locus identified by whole-exome sequencing. Eur J Hum Genet 25, 73-78 (2016).
Kerner, G. et al. A genome-wide case-only test for the detection of digenic inheritance in human exomes. Proc Natl Acad Sci U S A 117, 19367-19375 (2020).
Kim, D. Seung et al. Sequencing of sporadic Attention-Deficit Hyperactivity Disorder (ADHD) identifies novel and potentially pathogenic de novo variants and excludes overlap with genes associated with autism spectrum disorder. Am J Med Genet B Neuropsychiatr Genet 174, 381-389 (2017).
L
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).
Lee, W. et al. Complex inheritance of ABCA4 disease: four mutations in a family with multiple macular phenotypes. Hum Genet 135, 9-19 (2016).
Levinsohn, J. L., Sugarman, J. L., McNiff, J. M., Antaya, R. J. & Choate, K. A. Somatic Mutations in NEK9 Cause Nevus Comedonicus. Am J Hum Genet 98, 1030-1037 (2016).
Liu, D. J. & Leal, S. M. A unified method for detecting secondary trait associations with rare variants: application to sequence data. PLoS Genet 8, e1003075 (2012).
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).
M
Machol, K. et al. Corner fracture type spondylometaphyseal dysplasia: Overlap with type II collagenopathies. Am J Med Genet A 173, 733-739 (2017).
Mirzaa, G. M. et al. De novo and inherited variants in ZNF292 underlie a neurodevelopmental disorder with features of autism spectrum disorder. Genet Med 22, 538-546 (2020).
P
Palencia-Madrid, L. et al. Evaluation of the VISAGE Basic Tool for Appearance and Ancestry Prediction Using PowerSeq Chemistry on the MiSeq FGx System. Genes (Basel) 11, (2020).
Pehlivan, D. et al. Exome sequencing reveals homozygous TRIM2 mutation in a patient with early onset CMT and bilateral vocal cord paralysis. Hum Genet 134, 671-3 (2015).
Pehlivan, D. et al. The role of combined SNV and CNV burden in patients with distal symmetric polyneuropathy. Genet Med 18, 443-51 (2016).
Posey, J. E. et al. Molecular diagnostic experience of whole-exome sequencing in adult patients. Genet Med 18, 678-85 (2016).
Posey, J. E. et al. Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation. N Engl J Med 376, 21-31 (2017).
R
Rehm, H. L. Evolving health care through personal genomics. Nat Rev Genet 18, 259-267 (2017).
Rehman, A. U. et al. Challenges and solutions for gene identification in the presence of familial locus heterogeneity. Eur J Hum Genet 23, 1207-15 (2015).
Reid, J. G. et al. Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline. BMC Bioinformatics 15, 30 (2014).
Rosenthal, E. A. et al. Association Between Absolute Neutrophil Count and Variation at TCIRG1: The NHLBI Exome Sequencing Project. Genet Epidemiol 40, 470-4 (2016).
S
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).
Sambrotta, M. et al. Mutations in TJP2 cause progressive cholestatic liver disease. Nat Genet 46, 326-8 (2014).
Sethi, A. et al. Reads meet rotamers: structural biology in the age of deep sequencing. Curr Opin Struct Biol 35, 125-34 (2015).

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