ParseCNV2: efficient sequencing tool for genome-wide copy number variation association studies

  • Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SF, et al. PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole genome SNP genotyping data. Genome Res. 2007;17:1665–74.

    CAS PubMed Article PubMed Central Google Scholar

  • Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. Second Generation PLINK: Meeting the Challenge of Larger and Richer Datasets. Gigascience 2015;4:7.

    PubMed Article PubMed Central Google Scholar

  • Glessner JT, Li J, Hakonarson H. ParseCNV integrative copy number variation association software with quality tracking. Nucleic Acids Res. 2013;41:e64.

    CAS PubMed Article PubMed Central Google Scholar

  • Glessner JT, Wang K, Cai G, Korvatska O, Kim CE, Wood S, et al. Autism genome-wide copy number variation reveals ubiquitin and neural genes. Nature 2009;459:569–73.

    CAS PubMed Article PubMed Central Google Scholar

  • Mace A, Tuke MA, Beckmann JS, Lin L, Jacquemont S, Weedon MN, et al. New quality metric for CNV detection based on SNP matrix. Bioinformatics 2016;32:3298–305.

    CAS PubMed Google Scholar Article

  • Glessner JT, Hou X, Zhong C, Zhang J, Khan M, Brand F, et al. DeepCNV: A deep learning approach to authenticate copy number variations. Brief Bioinform. 2021.

  • Kim JH, Hu HJ, Yim SH, Bae JS, Kim SY, Chung YJ. CNVRuler: a case-control association analysis tool based on copy number variation. Bioinformatics 2012;28:1790–2.

    CAS PubMed Google Scholar Article

  • Zhan X, Hu Y, Li B, Abecasis GR, Liu DJ. RVTESTS: An efficient and comprehensive tool for association analysis of rare variants using sequence data. Bioinformatics 2016;32:1423–6.

    CAS PubMed Article PubMed Central Google Scholar

  • MacDonald JR, Ziman R, Yuen RK, Feuk L, Scherer SW. The Genomic Variant Database: a curated collection of structural variations in the human genome. Nucleic Acids Res 2014;42:D986–92.

    CAS PubMed Google Scholar Article

  • Collins RL, Brand H, Karczewski KJ, Zhao X, Alfoldi J, Francioli LC, et al. A structural variation reference for medical and population genetics. Nature 2020;581:444–51.

    CAS PubMed Article PubMed Central Google Scholar

  • Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, et al. An integrated map of structural variation in 2,504 human genomes. Nature 2015;526:75–81.

    CAS PubMed Article PubMed Central Google Scholar

  • Werling DM, Brand H, An JY, Stone MR, Zhu L, Glessner JT, et al. An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorders. Nat Genet. 2018;50:727–36.

    CAS PubMed Article PubMed Central Google Scholar

  • Zhan X, Girirajan S, Zhao N, Wu MC, Ghosh D. A new core association test of copy number variants with application to studies of autism spectrum disorders. Bioinformatics 2016;32:3603–10.

    CAS PubMed PubMed Central Google Scholar

  • Alexander-Bloch A, Huguet G, Schultz LM, Huffnagle N, Jacquemont S, Seidlitz J, et al. Copy variant risk scores associated with cognition, psychopathology, and brain structure in youth from the Philadelphia Neurodevelopmental Cohort. JAMA Psychiatry 2022;79:699–709.

    PubMed Article PubMed Central Google Scholar

  • Collins RL, Glessner JT, Porcu E, Lepamets M, Brandon R, Lauricella C, et al. A dose-sensitivity map of human genome cross-disorders. Cell 2022;185:3041–55.e25.

    CAS PubMed Google Scholar Article

  • Erikson GA, Deshpande N, Kesavan BG, Torkamani A. SG-ADVISER CNV: Copy number variant annotation and interpretation. Genet Med. 2015;17:714–8.

    PubMed Google Scholar article

  • Geoffroy V, Herenger Y, Kress A, Stoetzel C, Piton A, Dollfus H, et al. AnnotSV: an integrated tool for annotating structural variations. Bioinformatics 2018;34:3572–4.

    CAS PubMed Google Scholar Article

  • Glessner JT, Bick AG, Ito K, Homsy J, Rodriguez-Murillo L, Fromer M, et al. Increasing the frequency of de novo copy number variants in congenital heart disease by integrative analysis of single nucleotide polymorphism array and exome sequence data. Circ Res. 2014;115:884–96.

    CAS PubMed Article PubMed Central Google Scholar

  • Fromer M, Purcell SM. Using XHMM software to detect copy number variation in whole exome sequencing data. Curr Protoc Hum Genet. 2014;81:7 23 1–1.

    Google Scholar

  • Elia J, Glessner JT, Wang K, Takahashi N, Shtir CJ, Hadley D, et al. A genome-wide copy number variation study links metabotropic glutamate receptor gene networks to attention deficit hyperactivity disorder. Nat Genet. 2011;44:78–84.

    PubMed Article PubMed Central Google Scholar

  • Aguirre M, Rivas MA, Priest J. Charge of phenome-wide copy number variation in the UK biobank. Am J Hum Genet. 2019;105:373–83.

    CAS PubMed Article PubMed Central Google Scholar

  • Li YR, Glessner JT, Coe BP, Li J, Mohebnasab M, Chang X, et al. Rare copy number variants in more than 100,000 subjects of European ancestry reveal multiple disease associations. Common Nat. 2020;11:1–9.

    Google Scholar

  • Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, et al. Cross-platform discovery of haplotype-resolved structural variation in human genomes. Common Nat. 2019;10:1784.

    PubMed Article PubMed Central Google Scholar

  • Greenside P, Zook J, Salit M, Cule M, Poplin R, DePristo M. CrowdVariant: A crowdsourced approach to rank copy number variants. Pac Symp Biocomput. 2019;24:224–35.

    Google Scholar PubMed

  • Conway JR, Lex A, Gehlenborg N. UpSetR: An R package for visualizing intersecting sets and their properties. Bioinformatics 2017;33:2938–40.

    CAS PubMed Article PubMed Central Google Scholar

  • Comments are closed.