Identifying patterns of copy number variants in casecontrol studies of human genetic disorders

Abdullah K. Alqallafl, Ahmed H. Tewfik, Paula Krakowiak, Flora Tassone, Ryan Davis, Robin L Hansen, Irva Hertz-Picciotto, Isaac N Pessah, Jeffrey Gregg, Scott B. Selleck

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

DNA copy number variations are now recognized as an important contributor to human genetic disease. In this paper, our focus is on identifying patterns of DNA copy number variation detected with finely-tiled oligonucleotide arrays in casecontrol studies. This analysis is based on the observation that CNVs across large segments of the genome show recurring patterns, particularly in regions that bear repeat sequences that contribute to the genetic instability of that interval. The goal of this analysis is to increase the power to identify diseaseassociated genetic changes in case-controls studies of copy number variation. We propose a framework to evaluate the predictive power of recurrent variations at multiple genomic sites. First, we present a novel method based on maximum likelihood principle to clearly map and detect copy number variations along the studied genomic segments. Second, we apply regional analysis to evaluate the statistical and biological significance of recurrent variations followed by clustering methods to classify the tested samples. Finally, our results show that using the concatenated recurrent variant regions will considerably increase classification performance when compared with the traditional classifiers that use the entire data set. The results also provide insight into the pattern of the variations that may have a direct role in the targeted disease and can be used to improve diagnostic reliability for complex human genetic disorders.

Original languageEnglish (US)
Title of host publication2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009
DOIs
StatePublished - 2009
Event2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009 - Minneapolis, MN, United States
Duration: May 17 2009May 21 2009

Other

Other2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009
CountryUnited States
CityMinneapolis, MN
Period5/17/095/21/09

Fingerprint

DNA Copy Number Variations
Inborn Genetic Diseases
Medical Genetics
DNA
Oligonucleotides
Oligonucleotide Array Sequence Analysis
Maximum likelihood
Cluster Analysis
Case-Control Studies
Classifiers
Genes
Genome

ASJC Scopus subject areas

  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Vision and Pattern Recognition
  • Biomedical Engineering

Cite this

Alqallafl, A. K., Tewfik, A. H., Krakowiak, P., Tassone, F., Davis, R., Hansen, R. L., ... Selleck, S. B. (2009). Identifying patterns of copy number variants in casecontrol studies of human genetic disorders. In 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009 [5174366] https://doi.org/10.1109/GENSIPS.2009.5174366

Identifying patterns of copy number variants in casecontrol studies of human genetic disorders. / Alqallafl, Abdullah K.; Tewfik, Ahmed H.; Krakowiak, Paula; Tassone, Flora; Davis, Ryan; Hansen, Robin L; Hertz-Picciotto, Irva; Pessah, Isaac N; Gregg, Jeffrey; Selleck, Scott B.

2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009. 2009. 5174366.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Alqallafl, AK, Tewfik, AH, Krakowiak, P, Tassone, F, Davis, R, Hansen, RL, Hertz-Picciotto, I, Pessah, IN, Gregg, J & Selleck, SB 2009, Identifying patterns of copy number variants in casecontrol studies of human genetic disorders. in 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009., 5174366, 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009, Minneapolis, MN, United States, 5/17/09. https://doi.org/10.1109/GENSIPS.2009.5174366
Alqallafl AK, Tewfik AH, Krakowiak P, Tassone F, Davis R, Hansen RL et al. Identifying patterns of copy number variants in casecontrol studies of human genetic disorders. In 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009. 2009. 5174366 https://doi.org/10.1109/GENSIPS.2009.5174366
Alqallafl, Abdullah K. ; Tewfik, Ahmed H. ; Krakowiak, Paula ; Tassone, Flora ; Davis, Ryan ; Hansen, Robin L ; Hertz-Picciotto, Irva ; Pessah, Isaac N ; Gregg, Jeffrey ; Selleck, Scott B. / Identifying patterns of copy number variants in casecontrol studies of human genetic disorders. 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009. 2009.
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