Publications

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A
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).
English, A. C. et al. Assessing structural variation in a personal genome-towards a human reference diploid genome. BMC Genomics 16, 286 (2015).
Chen, L. et al. Association of structural variation with cardiometabolic traits in Finns. Am J Hum Genet 108, 583-596 (2021).
Yu, J. - H., Harrell, T. M., Jamal, S. M., Tabor, H. K. & Bamshad, M. J. Attitudes of genetics professionals toward the return of incidental results from exome and whole-genome sequencing. Am J Hum Genet 95, 77-84 (2014).
Yu, J. - H., Crouch, J., Jamal, S. M., Bamshad, M. J. & Tabor, H. K. Attitudes of non-African American focus group participants toward return of results from exome and whole genome sequencing. Am J Med Genet A 164A, 2153-60 (2014).
C
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).
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).
Scott, E. M. et al. Characterization of Greater Middle Eastern genetic variation for enhanced disease gene discovery. Nat Genet 48, 1071-6 (2016).
Fiallos, K. et al. Choices for return of primary and secondary genomic research results of 790 members of families with Mendelian disease. Eur J Hum Genet 25, 530-537 (2017).
Garg, S. et al. Chromosome-scale, haplotype-resolved assembly of human genomes. Nat Biotechnol 39, 309-312 (2021).
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).
Lupski, J. R. Clinical genomics: from a truly personal genome viewpoint. Hum Genet 135, 591-601 (2016).
Luo, X. et al. Clinically severe CACNA1A alleles affect synaptic function and neurodegeneration differentially. PLoS Genet 13, e1006905 (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).
Yuan, B. et al. Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates. PLoS Genet 11, e1005686 (2015).
D
Salzberg, S. L., Pertea, M., Fahrner, J. A. & Sobreira, N. DIAMUND: direct comparison of genomes to detect mutations. Hum Mutat 35, 283-8 (2014).
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).
E
Zhang, L. et al. Efficient CNV breakpoint analysis reveals unexpected structural complexity and correlation of dosage-sensitive genes with clinical severity in genomic disorders. Hum Mol Genet 26, 1927-1941 (2017).
Rubinacci, S., Ribeiro, D. M., Hofmeister, R. J. & Delaneau, O. Efficient phasing and imputation of low-coverage sequencing data using large reference panels. Nat Genet 53, 120-126 (2021).
Rehm, H. L. Evolving health care through personal genomics. Nat Rev Genet 18, 259-267 (2017).
F
Preuss, C. et al. Family Based Whole Exome Sequencing Reveals the Multifaceted Role of Notch Signaling in Congenital Heart Disease. PLoS Genet 12, e1006335 (2016).
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Qiao, D. et al. Gene-based segregation method for identifying rare variants in family-based sequencing studies. Genet Epidemiol 41, 309-319 (2017).
Kircher, M. et al. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 46, 310-5 (2014).
Ott, J., Wang, J. & Leal, S. M. Genetic linkage analysis in the age of whole-genome sequencing. Nat Rev Genet 16, 275-84 (2015).
H
Ebert, P. et al. Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science 372, (2021).
Hamdan, F. F. et al. High Rate of Recurrent De Novo Mutations in Developmental and Epileptic Encephalopathies. Am J Hum Genet 101, 664-685 (2017).
Gonzaga-Jauregui, C., Lupski, J. R. & Gibbs, R. A. Human genome sequencing in health and disease. Annu Rev Med 63, 35-61 (2012).
I
Gambin, T. et al. Identification of novel candidate disease genes from de novo exonic copy number variants. Genome Med 9, 83 (2017).
Bick, A. G. et al. Inherited causes of clonal haematopoiesis in 97,691 whole genomes. Nature 586, 763-768 (2020).
Posey, J. E. et al. Insights into genetics, human biology and disease gleaned from family based genomic studies. Genet Med 21, 798-812 (2019).
Boycott, K. M. et al. International Cooperation to Enable the Diagnosis of All Rare Genetic Diseases. Am J Hum Genet 100, 695-705 (2017).
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Wang, Q. et al. Landscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes. Nat Commun 11, 2539 (2020).
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Abel, H. J. et al. Mapping and characterization of structural variation in 17,795 human genomes. Nature 583, 83-89 (2020).
Gu, S. et al. Mechanisms for the Generation of Two Quadruplications Associated with Split-Hand Malformation. Hum Mutat 37, 160-4 (2016).
Carvalho, C. M. B. & Lupski, J. R. Mechanisms underlying structural variant formation in genomic disorders. Nat Rev Genet 17, 224-38 (2016).
Posey, J. E. et al. Molecular diagnostic experience of whole-exome sequencing in adult patients. Genet Med 18, 678-85 (2016).
Campbell, I. M. et al. Multiallelic Positions in the Human Genome: Challenges for Genetic Analyses. Hum Mutat 37, 231-234 (2016).
Karczewski, K. J. et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434-443 (2020).
Jin, S. Chih et al. Mutations disrupting neuritogenesis genes confer risk for cerebral palsy. Nat Genet 52, 1046-1056 (2020).
N
Yuan, B. et al. Nonrecurrent 17p11.2p12 Rearrangement Events that Result in Two Concomitant Genomic Disorders: The PMP22-RAI1 Contiguous Gene Duplication Syndrome. Am J Hum Genet 97, 691-707 (2015).
P
Szafranski, P. et al. Pathogenetics of alveolar capillary dysplasia with misalignment of pulmonary veins. Hum Genet 135, 569-586 (2016).
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).
Fahed, A. C. et al. Polygenic background modifies penetrance of monogenic variants for tier 1 genomic conditions. Nat Commun 11, 3635 (2020).
Song, X. et al. Predicting human genes susceptible to genomic instability associated with /-mediated rearrangements. Genome Res 28, 1228-1242 (2018).
R
Shen, F. & Kidd, J. M. Rapid, Paralog-Sensitive CNV Analysis of 2457 Human Genomes Using QuicK-mer2. Genes (Basel) 11, (2020).
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Freeze, H. H., Chong, J. X., Bamshad, M. J. & Ng, B. G. Solving glycosylation disorders: fundamental approaches reveal complicated pathways. Am J Hum Genet 94, 161-75 (2014).
Campbell, I. M., Shaw, C. A., Stankiewicz, P. & Lupski, J. R. Somatic mosaicism: implications for disease and transmission genetics. Trends Genet 31, 382-92 (2015).
Dashnow, H. et al. STRetch: detecting and discovering pathogenic short tandem repeat expansions. Genome Biol 19, 121 (2018).
Lupski, J. R. Structural variation mutagenesis of the human genome: Impact on disease and evolution. Environ Mol Mutagen 56, 419-36 (2015).
Collins, R. L. et al. A structural variation reference for medical and population genetics. Nature 581, 444-451 (2020).

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