Publications

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2011
Lupski, J. R., Belmont, J. W., Boerwinkle, E. & Gibbs, R. A. Clan genomics and the complex architecture of human disease. Cell 147, 32-43 (2011).
2012
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).
Mechanic, L. E. et al. Next generation analytic tools for large scale genetic epidemiology studies of complex diseases. Genet Epidemiol 36, 22-35 (2012).
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).
Li, B., Wang, G. & Leal, S. M. SimRare: a program to generate and analyze sequence-based data for association studies of quantitative and qualitative traits. Bioinformatics 28, 2703-4 (2012).
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).
2013
Kambur, O. et al. Effect of catechol-o-methyltransferase-gene (COMT) variants on experimental and acute postoperative pain in 1,000 women undergoing surgery for breast cancer. Anesthesiology 119, 1422-33 (2013).
Carvalho, C. M. B. et al. Replicative mechanisms for CNV formation are error prone. Nat Genet 45, 1319-26 (2013).
2014
Salzberg, S. L., Pertea, M., Fahrner, J. A. & Sobreira, N. DIAMUND: direct comparison of genomes to detect mutations. Hum Mutat 35, 283-8 (2014).
Kircher, M. et al. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 46, 310-5 (2014).
Wang, G. T., Li, B., Santos-Cortez, R. P. Lyn, Peng, B. & Leal, S. M. Power analysis and sample size estimation for sequence-based association studies. Bioinformatics 30, 2377-8 (2014).
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).
Cecchi, A. C. et al. RNF213 rare variants in an ethnically diverse population with Moyamoya disease. Stroke 45, 3200-7 (2014).
Wang, G. T., Peng, B. & Leal, S. M. Variant association tools for quality control and analysis of large-scale sequence and genotyping array data. Am J Hum Genet 94, 770-83 (2014).
2015
Gonzaga-Jauregui, C. et al. Exome Sequence Analysis Suggests that Genetic Burden Contributes to Phenotypic Variability and Complex Neuropathy. Cell Rep 12, 1169-83 (2015).
Fairfield, H. et al. Exome sequencing reveals pathogenic mutations in 91 strains of mice with Mendelian disorders. Genome Res 25, 948-57 (2015).
Sobreira, N., Schiettecatte, F., Valle, D. & Hamosh, A. GeneMatcher: a matching tool for connecting investigators with an interest in the same gene. Hum Mutat 36, 928-30 (2015).
Karaca, E. et al. Genes that Affect Brain Structure and Function Identified by Rare Variant Analyses of Mendelian Neurologic Disease. Neuron 88, 499-513 (2015).
Sobreira, N., Schiettecatte, F., Boehm, C., Valle, D. & Hamosh, A. New tools for Mendelian disease gene identification: PhenoDB variant analysis module; and GeneMatcher, a web-based tool for linking investigators with an interest in the same gene. Hum Mutat 36, 425-31 (2015).
Zhang, F. & Lupski, J. R. Non-coding genetic variants in human disease. Hum Mol Genet 24, R102-10 (2015).
Cogan, J. D. et al. Rare variants in RTEL1 are associated with familial interstitial pneumonia. Am J Respir Crit Care Med 191, 646-55 (2015).
2016
Scott, E. M. et al. Characterization of Greater Middle Eastern genetic variation for enhanced disease gene discovery. Nat Genet 48, 1071-6 (2016).
Lupski, J. R. Clinical genomics: from a truly personal genome viewpoint. Hum Genet 135, 591-601 (2016).
White, J. J. et al. DVL3 Alleles Resulting in a -1 Frameshift of the Last Exon Mediate Autosomal-Dominant Robinow Syndrome. Am J Hum Genet 98, 553-561 (2016).
Wang, L. et al. Family-Based Rare Variant Association Analysis: A Fast and Efficient Method of Multivariate Phenotype Association Analysis. Genet Epidemiol 40, 502-11 (2016).
Choi, S. et al. FARVATX: Family-Based Rare Variant Association Test for X-Linked Genes. Genet Epidemiol 40, 475-85 (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).
Yazdani, A., Yazdani, A., Liu, X. & Boerwinkle, E. Identification of Rare Variants in Metabolites of the Carnitine Pathway by Whole Genome Sequencing Analysis. Genet Epidemiol 40, 486-91 (2016).
Sul, J. Hoon et al. Increasing Generality and Power of Rare-Variant Tests by Utilizing Extended Pedigrees. Am J Hum Genet 99, 846-859 (2016).
Kumar, S., Clarke, D. & Gerstein, M. Localized structural frustration for evaluating the impact of sequence variants. Nucleic Acids Res 44, 10062-10073 (2016).
Yu, B. et al. Loss-of-function variants influence the human serum metabolome. Sci Adv 2, e1600800 (2016).
Guo, D. - C. et al. LOX Mutations Predispose to Thoracic Aortic Aneurysms and Dissections. Circ Res 118, 928-34 (2016).
Carvalho, C. M. B. & Lupski, J. R. Mechanisms underlying structural variant formation in genomic disorders. Nat Rev Genet 17, 224-38 (2016).
Harel, T. et al. Monoallelic and Biallelic Variants in EMC1 Identified in Individuals with Global Developmental Delay, Hypotonia, Scoliosis, and Cerebellar Atrophy. Am J Hum Genet 98, 562-570 (2016).
Yu, H. et al. Rapid molecular diagnostics of severe primary immunodeficiency determined by using targeted next-generation sequencing. J Allergy Clin Immunol 138, 1142-1151.e2 (2016).
O'Grady, G. L. et al. Variants in SLC18A3, vesicular acetylcholine transporter, cause congenital myasthenic syndrome. Neurology 87, 1442-1448 (2016).
O'Grady, G. L. et al. Variants in the Oxidoreductase PYROXD1 Cause Early-Onset Myopathy with Internalized Nuclei and Myofibrillar Disorganization. Am J Hum Genet 99, 1086-1105 (2016).
James, R. A. et al. A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics. Genome Med 8, 13 (2016).
Farlow, J. L. et al. Whole-Exome Sequencing in Familial Parkinson Disease. JAMA Neurol 73, 68-75 (2016).
2017
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).
Turner, T. N. et al. denovo-db: a compendium of human de novo variants. Nucleic Acids Res 45, D804-D811 (2017).
Qiao, D. et al. Gene-based segregation method for identifying rare variants in family-based sequencing studies. Genet Epidemiol 41, 309-319 (2017).
Johnson, K. et al. Identification of GAA variants through whole exome sequencing targeted to a cohort of 606 patients with unexplained limb-girdle muscle weakness. Orphanet J Rare Dis 12, 173 (2017).
Miszalski-Jamka, K. et al. Novel Genetic Triggers and Genotype-Phenotype Correlations in Patients With Left Ventricular Noncompaction. Circ Cardiovasc Genet 10, (2017).
Kropski, J. A. et al. Rare Genetic Variants in PARN Are Associated with Pulmonary Fibrosis in Families. Am J Respir Crit Care Med 196, 1481-1484 (2017).
Schoch, K. et al. A Recurrent De Novo Variant in NACC1 Causes a Syndrome Characterized by Infantile Epilepsy, Cataracts, and Profound Developmental Delay. Am J Hum Genet 100, 343-351 (2017).
Posey, J. E. et al. Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation. N Engl J Med 376, 21-31 (2017).
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).
2018
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).
Johnson, K. et al. Detection of variants in dystroglycanopathy-associated genes through the application of targeted whole-exome sequencing analysis to a large cohort of patients with unexplained limb-girdle muscle weakness. Skelet Muscle 8, 23 (2018).

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