An Optimization Framework for Unsupervised Identification of Rare Copy Number Variation from SNP Array Data

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2009 Oct 24

PMID 19849861

Citations 14

Authors

Gokhan Yavas

Mehmet Koyuturk

Meral Ozsoyoglu

Meetha P Gould

Thomas LaFramboise

Affiliations

Soon will be listed here.

Abstract

Copy number variants (CNVs) have roles in human disease, and DNA microarrays are important tools for identifying them. In this paper, we frame CNV identification as an objective function optimization problem. We apply our method to data from hundreds of samples, and demonstrate its ability to detect CNVs at a high level of sensitivity without sacrificing specificity. Its performance compares favorably with currently available methods and it reveals previously unreported gains and losses.

Citing Articles

Truvari: refined structural variant comparison preserves allelic diversity.

English A, Menon V, Gibbs R, Metcalf G, Sedlazeck F Genome Biol. 2022; 23(1):271.

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Genomic Structural Diversity in Local Goats: Analysis of Copy-Number Variations.

Di Gerlando R, Mastrangelo S, Moscarelli A, Tolone M, Sutera A, Portolano B Animals (Basel). 2020; 10(6).

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Deciphering the chronology of copy number alterations in Multiple Myeloma.

Aktas Samur A, Minvielle S, Shammas M, Fulciniti M, Magrangeas F, Richardson P Blood Cancer J. 2019; 9(4):39.

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Copy number variation in livestock: A mini review.

Bhanuprakash V, Chhotaray S, Pruthviraj D, Rawat C, Karthikeyan A, Panigrahi M Vet World. 2018; 11(4):535-541.

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Post-zygotic genomic changes in glutamate and dopamine pathway genes may explain discordance of monozygotic twins for schizophrenia.

Castellani C, Melka M, Gui J, Gallo A, OReilly R, Singh S Clin Transl Med. 2017; 6(1):43.

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