Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

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Evolutionary Rate at the Molecular Level

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Functional Characterization Reveals the Significance of Rare Coding Variations in Human Organic Anion Transporting Polypeptide 2B1 (SLCO2B1)

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Rare Variants in PLXNA4 and Parkinson’s Disease

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An evolutionary perspective on complex neuropsychiatric disease

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Pathway‐Based Approaches for Sequencing‐Based Genome‐Wide Association Studies

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Discriminating between deleterious and neutral non-frameshifting indels based on protein interaction networks and hybrid properties

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Transcriptome sequencing of Chinese and Caucasian population identifies ethnic-associated differential transcript abundance of heterogeneous nuclear ribonucleoprotein K (hnRNPK)

Li, J., Lai, K. P., Ching, A. K.-K., & Chan, T.-F. (2014) · Genomics · doi:10.1016/j.ygeno.2013.12.005 · Cited by 23

Impact of exome sequencing in inflammatory bowel disease

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Next-generation sequencing-based molecular diagnosis of 12 inherited retinal disease probands of Uyghur ethnicity

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Quantitative mapping of DNA phosphorothioatome reveals phosphorothioate heterogeneity of low modification frequency

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von Willebrand factor antigen levels are associated with burden of rare nonsynonymous variants in the VWF gene

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Alpha-1 Antitrypsin and Hepatocellular Carcinoma in Liver Cirrhosis: SERPINA1 MZ or MS Genotype Carriage Decreases the Risk

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Systems biology analysis of human genomes points to key pathways conferring spina bifida risk

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This population does not exist: learning the distribution of evolutionary histories with generative adversarial networks

Booker, W. W., Ray, D. D., & Schrider, D. R. (2023) · GENETICS · doi:10.1093/genetics/iyad063 · Cited by 22

Interlocus gene conversion explains at least 2.7 % of single nucleotide variants in human segmental duplications

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Rare Titin (TTN) Variants in Diseases Associated with Sudden Cardiac Death

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Analysis of Human Triallelic SNPs by Next‐Generation Sequencing

Cao, M., Shi, J., Wang, J., Hong, J., Cui, B., & Ning, G. (2015) · Annals of Human Genetics · doi:10.1111/ahg.12114 · Cited by 22

No Gene in the Genome Makes Sense Except in the Light of Evolution

Haerty, W., & Ponting, C. P. (2014) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-090413-025621 · Cited by 21

CEDNIK

Hsu, T., Coughlin, C. C., Monaghan, K. G., Fiala, E. M., McKinstry, R. C., Paciorkowski, A. R., & Shinawi, M. S. (2017) · Child Neurology Open · doi:10.1177/2329048x17733214 · Cited by 22

Genetic Testing for Cardiomyopathies in Clinical Practice

Ingles, J., Bagnall, R. D., & Semsarian, C. (2018) · Heart Failure Clinics · doi:10.1016/j.hfc.2017.12.001 · Cited by 22

Prioritization of Variants Detected by Next Generation Sequencing According to the Mutation Tolerance and Mutational Architecture of the Corresponding Genes

Roca, I., Marmiesse, A. F., Gouveia, S., Segovia, M., & Couce, M. L. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19061584 · Cited by 22

Structural variation at the CYP2C locus: Characterization of deletion and duplication alleles

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Mutation severity spectrum of rare alleles in the human genome is predictive of disease type

Pei, J., Kinch, L. N., Otwinowski, Z., & Grishin, N. V. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007775 · Cited by 21

Identification of potential causal variants for premature ovarian failure by whole exome sequencing

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Exomic Sequencing of Immune-Related Genes Reveals Novel Candidate Variants Associated with Alopecia Universalis

Lee, S., Paik, S. H., Kim, H. J., Ryu, H. H., Cha, S., Jo, S. J., Eun, H. C., Seo, J., Kim, J., & Kwon, O. (2013) · PLoS ONE · doi:10.1371/journal.pone.0053613 · Cited by 23

Genetic associations of nonsynonymous exonic variants with psychophysiological endophenotypes

Vrieze, S. I., Malone, S. M., Pankratz, N., Vaidyanathan, U., Miller, M. B., Kang, H. M., McGue, M. K., Abecasis, G. R., & Iacono, W. G. (2014) · Psychophysiology · doi:10.1111/psyp.12349 · Cited by 21

Analysis of rare variant population structure in Europeans explains differential stratification of gene-based tests

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Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts

Hakenberg, J., Cheng, W., Thomas, P. E., Wang, Y., Uzilov, A. V., & Chen, R. (2016) · BMC Bioinformatics · doi:10.1186/s12859-015-0865-9 · Cited by 21

Genetic association studies in cardiovascular diseases: Do we have enough power?

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The Genetic Control of the Rheumatic Heart: Closing the Genotype-Phenotype Gap

Abdallah, A. M., & Abu-Madi, M. A. (2021) · Frontiers in Medicine · doi:10.3389/fmed.2021.611036 · Cited by 21

Integrating Massively Parallel Sequencing into Diagnostic Workflows and Managing the Annotation and Clinical Interpretation Challenge

Kassahn, K. S., Scott, H. S., & Caramins, M. C. (2014) · Human Mutation · doi:10.1002/humu.22525 · Cited by 22

Detection and correction of artefacts in estimation of rare copy number variants and analysis of rare deletions in type 1 diabetes

Cooper, N. J., Shtir, C. J., Smyth, D. J., Guo, H., Swafford, A. D.-E., Zanda, M., Hurles, M. E., Walker, N. M., Plagnol, V., Cooper, J. D., et al. (2014) · Human Molecular Genetics · doi:10.1093/hmg/ddu581 · Cited by 20

Evolutionary Balancing Is Critical for Correctly Forecasting Disease-Associated Amino Acid Variants

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Power analysis and sample size estimation for sequence-based association studies

Wang, G. T., Li, B., Santos-Cortez, R. P. L., Peng, B., & Leal, S. M. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu296 · Cited by 21

Global Carrier Rates of Rare Inherited Disorders Using Population Exome Sequences

Fujikura, K. (2016) · PLoS ONE · doi:10.1371/journal.pone.0155552 · Cited by 20

Diagnostic evaluation of RNA sequencing for the detection of genetic abnormalities associated with Ph-like acute lymphoblastic leukemia (ALL)

Yap, K. L., Furtado, L. V., Kiyotani, K., Curran, E. K., Stock, W., McNeer, J. L., Kadri, S., Segal, J. P., Nakamura, Y., Beau, M. M. L., et al. (2016) · Leukemia & lymphoma/Leukemia and lymphoma · doi:10.1080/10428194.2016.1219902 · Cited by 21

AIM-SNPtag: A computationally efficient approach for developing ancestry-informative SNP panels

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Localized structural frustration for evaluating the impact of sequence variants

Kumar, S., Clarke, D., & Gerstein, M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkw927 · Cited by 21

A linked‐read approach to museomics: Higher quality de novo genome assemblies from degraded tissues

Colella, J. P., Tigano, A., & MacManes, M. D. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13155 · Cited by 22

Co-barcoded sequence reads from long DNA fragments: a cost-effective solution for “perfect genome” sequencing

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SimRare: a program to generate and analyze sequence-based data for association studies of quantitative and qualitative traits

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Dissecting mammalian immunity through mutation

Siggs, O. M. (2014) · Immunology & Cell Biology · doi:10.1038/icb.2014.8 · Cited by 20

Tracing the Evolution of Human Immunity Through Ancient DNA

Patin, É., & Quintana‐Murci, L. (2024) · Annual Review of Immunology · doi:10.1146/annurev-immunol-082323-024638 · Cited by 21

AMELY deletion is not detected in systematically sampled reference populations: A Reply to Štamfelj

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Human gain-of-function variants in HNF1A confer protection from diabetes but independently increase hepatic secretion of atherogenic lipoproteins

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A novel mutation in the TMC1 gene causes non-syndromic hearing loss in a Moroccan family.

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Quantitative group testing-based overlapping pool sequencing to identify rare variant carriers

Cao, C., Li, C., & Sun, X. S. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-195 · Cited by 20

Detection and Impact of Rare Regulatory Variants in Human Disease

Li, X., & Montgomery, S. B. (2013) · Frontiers in Genetics · doi:10.3389/fgene.2013.00067 · Cited by 20

GWASeq: targeted re-sequencing follow up to GWAS

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Combinatorial pooled sequencing: experiment design and decoding

Cao, C., & Sun, X. S. (2016) · Quantitative Biology · doi:10.1007/s40484-016-0064-3 · Cited by 20

Pharmacogenetics of Potassium Channel Blockers

Roden, D. M. (2016) · Cardiac Electrophysiology Clinics · doi:10.1016/j.ccep.2016.02.003 · Cited by 20

mirDNMR: a gene-centered database of backgroundde novomutation rates in human

Jiang, Y., Li, Z., Liu, Z., Chen, D., Wu, W., Du, Y., Ji, L., Jin, Z., Li, W., & Wu, J. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1044 · Cited by 19

Disease‐Concordant Twins Empower Genetic Association Studies

Tan, Q., Li, W., & Vandin, F. (2016) · Annals of Human Genetics · doi:10.1111/ahg.12181 · Cited by 20

A novel, homozygous nonsense variant of the CDHR1 gene in a Chinese family causes autosomal recessive retinal dystrophy by NGS‐based genetic diagnosis

Fu, J., Ma, L., Cheng, J., Yang, L., Wei, C., Fu, S., Lv, H., Chen, R., & Fu, J. (2018) · Journal of Cellular and Molecular Medicine · doi:10.1111/jcmm.13841 · Cited by 20

Naturally Segregating Variation at Ugt86Dd Contributes to Nicotine Resistance in Drosophila melanogaster

Highfill, C., Tran, J. H., Nguyen, S. K. T., Moldenhauer, T. R., Wang, X., & Macdonald, S. J. (2017) · Genetics · doi:10.1534/genetics.117.300058 · Cited by 21

Thousands of missing variants in the UK Biobank are recoverable by genome realignment

Jia, T., Munson, B. P., Allen, H. L., Ideker, T. E., & Majithia, A. R. (2020) · Annals of Human Genetics · doi:10.1111/ahg.12383 · Cited by 20

VarMod: modelling the functional effects of non-synonymous variants

Pappalardo, M., & Wass, M. N. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku483 · Cited by 20

Common Low-Density Lipoprotein Receptor p.G116S Variant Has a Large Effect on Plasma Low-Density Lipoprotein Cholesterol in Circumpolar Inuit Populations

Dubé, J. B., Wang, J., Cao, H., McIntyre, A. D., Johansen, C. T., Hopkins, S. E., Stringer, R., Hosseinzadeh, S., Kennedy, B. A., Ban, M. R., et al. (2014) · Circulation Cardiovascular Genetics · doi:10.1161/circgenetics.114.000646 · Cited by 21

Massive parallel sequencing questions the pathogenic role of missense variants in dilated cardiomyopathy

Dalin, M. G., Engström, P. G., Ivarsson, E. G., Unneberg, P., Light, S., Schaufelberger, M., Gilljam, T., Andersson, B., & Bergö, M. O. (2016) · International Journal of Cardiology · doi:10.1016/j.ijcard.2016.11.066 · Cited by 19

Linking Genes to Neurological Clinical Practice

Goldberg, A., Curtis, C. L., & Kleim, J. A. (2014) · Neurology Report · doi:10.1097/npt.0000000000000066 · Cited by 19

A Geometric Framework for Evaluating Rare Variant Tests of Association

Liu, K., Fast, S., Zawistowski, M., & Tintle, N. (2013) · Genetic Epidemiology · doi:10.1002/gepi.21722 · Cited by 19

INSPECTRE: Privately Estimating the Unseen

Acharya, J., Kamath, G., Sun, Z., & Zhang, H. (2020) · Journal of Privacy and Confidentiality · doi:10.29012/jpc.724 · Cited by 19

‘More than a box of puzzles’: Understanding the parental experience of having a child with a rare genetic condition"

Fitzgerald, J., Wilson, C. E., Kelly, C. A. M., & Gallagher, L. (2021) · European Journal of Medical Genetics · doi:10.1016/j.ejmg.2021.104164 · Cited by 23

Sex‐linked genetic diversity and differentiation in a globally distributed avian species complex

Schield, D. R., Scordato, E. S. C., Smith, C. C. R., Carter, J. K., Cherkaoui, S. I., Gombobaatar, S., Hajib, S., Hanane, S., Hund, A. K., Koyama, K., et al. (2021) · Molecular Ecology · doi:10.1111/mec.15885 · Cited by 19

von Willebrand disease and von Willebrand factor

Sadler, B. E., Castaman, G., & O’Donnell, J. S. (2022) · Haemophilia · doi:10.1111/hae.14547 · Cited by 19

A low-frequency GLIS3 variant associated with resistance to Japanese type 1 diabetes

Awata, T., Yamashita, H., Kurihara, S., Morita‐Ohkubo, T., Miyashita, Y., Katayama, S., Kawasaki, E., Tanaka, S. A., Ikegami, H., Maruyama, T., et al. (2013) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2013.06.102 · Cited by 19

QPLOT: A Quality Assessment Tool for Next Generation Sequencing Data

Li, B., Zhan, X., Wing, M. K., Anderson, P., Kang, H. M., & Abecasis, G. R. (2013) · BioMed Research International · doi:10.1155/2013/865181 · Cited by 20

The Lausanne Institutional Biobank: A new resource to catalyse research in personalised medicine and pharmaceutical sciences

Mooser, V., & Currat, C. (2014) · Swiss Medical Weekly · doi:10.4414/smw.2014.14033 · Cited by 21

The role of functional data in interpreting the effects of genetic variation

Young, D. L., & Fields, S. (2015) · Molecular Biology of the Cell · doi:10.1091/mbc.e15-03-0153 · Cited by 18

Functional Regression Models for Epistasis Analysis of Multiple Quantitative Traits

Zhang, F., Xie, D., Liang, M., & Xiong, M. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1005965 · Cited by 19

Coding-sequence variants are associated with blood lipid levels in 14,473 Chinese

Lu, X., Li, J., Li, H., Yang, C., Wang, L., He, M., Wang, Y., Sun, L. D., Hu, Y., Huang, J., et al. (2016) · Human Molecular Genetics · doi:10.1093/hmg/ddw261 · Cited by 19

Whole-genome sequencing suggests mechanisms for 22q11.2 deletion-associated Parkinson’s disease

Butcher, N. J., Merico, D., Zarrei, M., Ogura, L., Marshall, C. R., Chow, E. W. C., Lang, A. E., Scherer, S. W., & Bassett, A. S. (2017) · PLoS ONE · doi:10.1371/journal.pone.0173944 · Cited by 19

Utility of Population-Level DNA Sequence Data in the Diagnosis of Hereditary Endocrine Disease

Newey, P. J., Berg, J. N., Zhou, K., Palmer, C. N. A., & Thakker, R. V. (2017) · Journal of the Endocrine Society · doi:10.1210/js.2017-00330 · Cited by 19

Structural and Computational Characterization of Disease-Related Mutations Involved in Protein-Protein Interfaces

Navío, D., Rosell, M., Aguirre, J., de la Cruz, X., & Fernández‐Recio, J. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20071583 · Cited by 19

Genetic Factors Associated with a Poor Outcome in Head and Neck Cancer Patients Receiving Definitive Chemoradiotherapy

Vossen, D. M., Verhagen, C. V. M., van der Heijden, M., Essers, P., Bartelink, H. G. M. M., Verheij, M., Wessels, L. F. A., van den Brekel, M. W. M., & Vens, C. (2019) · Cancers · doi:10.3390/cancers11040445 · Cited by 18

Overcoming constraints on the detection of recessive selection in human genes from population frequency data

Balick, D. J., Jordan, D. M., Sunyaev, S. R., & Do, R. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.12.001 · Cited by 19

Establishing the role of rare coding variants in known Parkinson's disease risk loci

Jansen, I. E., Gibbs, J. R., Nalls, M. A., Price, T. R., Lubbe, S. J., van Rooij, J., Uitterlinden, A. G., Kraaij, R., Williams, N. M., Brice, A., et al. (2017) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2017.07.009 · Cited by 18

Evaluating the relevance of sequence conservation in the prediction of pathogenic missense variants

Capriotti, E., & Fariselli, P. (2022) · Human Genetics · doi:10.1007/s00439-021-02419-4 · Cited by 19

Whole-exome sequencing of 14 389 individuals from the ESP and CHARGE consortia identifies novel rare variation associated with hemostatic factors

Pankratz, N., Wei, P., Brody, J. A., Chen, M., de Vries, P. S., Huffman, J. E., Nalehua, M. R., Auer, P. L., Boerwinkle, E., Cushman, M., et al. (2022) · Human Molecular Genetics · doi:10.1093/hmg/ddac100 · Cited by 18

From SNP to pathway-based GWAS meta-analysis: do current meta-analysis approaches resolve power and replication in genetic association studies?

Defo, J., Awany, D., & Ramesar, R. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac600 · Cited by 20

The Use of Next-Generation Sequencing in Personalized Medicine

Popova, L., & Carabetta, V. J. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-4192-7_16 · Cited by 20

Methods for Association Analysis and Meta‐Analysis of Rare Variants in Families

Feng, S., Pistis, G., Zhang, H., Zawistowski, M., Mulas, A., Żołędziewska, M., Holmen, O. L., Busonero, F., Sanna, S., Hveem, K., et al. (2015) · Genetic Epidemiology · doi:10.1002/gepi.21892 · Cited by 20

Next generation sequencing and rare genetic variants: From human population studies to medical genetics

Matullo, G., Gaetano, C. D., & Guarrera, S. (2013) · Environmental and Molecular Mutagenesis · doi:10.1002/em.21799 · Cited by 21

The humankind genome: from genetic diversity to the origin of human diseases

Belizário, J. E. (2013) · Genome · doi:10.1139/gen-2013-0125 · Cited by 19

Predicting Signatures of “Synthetic Associations” and “Natural Associations” from Empirical Patterns of Human Genetic Variation

Chang, D., & Keinan, A. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002600 · Cited by 17

Exome Sequencing Identifies DLG1 as a Novel Gene for Potential Susceptibility to Crohn's Disease in a Chinese Family Study

Xu, S., Zhou, F., Tao, J., Song, L., Ng, S. C., Wang, X., Chen, L., Yi, F., Ran, Z., Zhou, R., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0099807 · Cited by 18

Uncovering the Rare Variants of DLC1 Isoform 1 and Their Functional Effects in a Chinese Sporadic Congenital Heart Disease Cohort

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Whole-exome imputation of sequence variants identified two novel alleles associated with adult body height in African Americans.

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(2014)

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