TITLE

LDx: Estimation of Linkage Disequilibrium from High-Throughput Pooled Resequencing Data

AUTHOR(S)
Feder, Alison F.; Petrov, Dmitri A.; Bergland, Alan O.
PUB. DATE
November 2012
SOURCE
PLoS ONE;Nov2012, Vol. 7 Issue 11, Special section p1
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
High-throughput pooled resequencing offers significant potential for whole genome population sequencing. However, its main drawback is the loss of haplotype information. In order to regain some of this information, we present LDx, a computational tool for estimating linkage disequilibrium (LD) from pooled resequencing data. LDx uses an approximate maximum likelihood approach to estimate LD (r²) between pairs of SNPs that can be observed within and among single reads. LDx also reports r² estimates derived solely from observed genotype counts. We demonstrate that the LDx estimates are highly correlated with r² estimated from individually resequenced strains. We discuss the performance of LDx using more stringent quality conditions and infer via simulation the degree to which performance can improve based on read depth. Finally we demonstrate two possible uses of LDx with real and simulated pooled resequencing data. First, we use LDx to infer genomewide patterns of decay of LD with physical distance in D. melanogaster population resequencing data. Second, we demonstrate that r² estimates from LDx are capable of distinguishing alternative demographic models representing plausible demographic histories of D. melanogaster.
ACCESSION #
84715395

 

Related Articles

  • Gene expression array profile of human osteosarcoma. Leonard, P.; Sharp, T.; Henderson, S.; Hewitt, D.; Pringle, J.; Sandison, A.; Goodship, A.; Whelan, J.; Boshoff, C. // British Journal of Cancer;12/15/2003, Vol. 89 Issue 12, p2284 

    The aims of this pilot study were to determine whether needle and open biopsies from osteosarcoma (OS) provide sufficient quality of mRNA for cDNA array analyses to gain insights into the expression profile of OS. A total of 22 samples collected from OS were used for array analyses. A primary...

  • Decreased expression of the DBC2 gene and its clinicopathological significance in breast cancer: correlation with aberrant DNA methylation. Han, Linlin; Hou, Lin; Song, Jinlian; Lin, Dongliang; Wu, Li; Ge, Yinlin; Ma, Zhongliang // Biotechnology Letters;Aug2013, Vol. 35 Issue 8, p1175 

    Loss of DBC2 (deleted in breast cancer 2) gene expression is frequent in breast cancer tissues. This can be explained by homozygous deletions or other mutations in a minority of cases but alternative mechanisms need to be investigated. Here, DBC2 expression was significantly suppressed compared...

  • Role of DNA Methylation in Cell Cycle Arrest Induced by Cr (VI) in Two Cell Lines. Lou, Jianlin; Wang, Yu; Yao, Chunji; Jin, Lingzhi; Wang, Xiuzhi; Xiao, Yun; Wu, Nanxiang; Song, Peng; Song, Yang; Tan, Yufeng; Gao, Ming; Liu, Kecheng; Zhang, Xing // PLoS ONE;Aug2013, Vol. 8 Issue 8, p1 

    Hexavalent chromium [Cr(IV)], a well-known industrial waste product and an environmental pollutant, is recognized as a human carcinogen. But its mechanisms of carcinogenicity remain unclear, and recent studies suggest that DNA methylation may play an important role in the carcinogenesis of...

  • The effects of DNA methylation and epigenetic factors on the expression of CD133 in ovarian cancers. Kyung-Jin Min; Kyeong A. So; Yung-Taek Ouh; Jin-Hwa Hong; Jae-Kwan Lee // Journal of Ovarian Research;2012, Vol. 5 Issue 1, p28 

    Background: To identifying the effects of DNA methylation and epigenetic factors on the expression of CD133, a cancer stem cell marker, in gynecologic cancer cell lines. Methods: Ovarian cancer cell lines (OVCAR-8 and IGROV-1) and an endometrial cancer cell line (Ishikawa) were treated with...

  • DNA hypermethylation of the vimentin gene inversely correlates with vimentin expression in intestinal- and diffuse-type gastric cancer. HUI CONG; RU-YONG YAO; ZHEN-QING SUN; WEN-SHENG QIU; YA-SAI YAO; TONG-TONG FENG; CHAO XIN; JUN LIANG; LU YUE // Oncology Letters;Jan2016, Vol. 11 Issue 1, p842 

    The vimentin gene is a hallmark of epithelial-to-mesenchymal transition and has been observed to be overexpressed in various types of tumor cell line and tissue. Previous studies have reported correlations between vimentin DNA methylation levels and subsequent vimentin expression levels in solid...

  • Down-regulation of ribosomal protein L7A in human osteosarcoma. Shui-er Zheng; Yang Yao; Yang Dong; Feng Lin; Hui Zhao; Zan Shen; Yuan-jue Sun; Li-na Tang // Journal of Cancer Research & Clinical Oncology;Aug2009, Vol. 135 Issue 8, p1025 

    To explore the expression of ribosomal protein L7A (RPL7A) in osteosarcoma and its correlation with clinical features. Ribosomal protein L7A mRNA expression was quantified by real-time reverse transcription (RT)-polymerase chain reaction (PCR) in 47 specimens from osteosarcoma, 8 from normal...

  • Integrative DNA Methylation and Gene Expression Analyses Identify DNA Packaging and Epigenetic Regulatory Genes Associated with Low Motility Sperm. Pacheco, Sara E.; Houseman, E. Andres; Christensen, Brock C.; Marsit, Carmen J.; Kelsey, Karl T.; Sigman, Mark; Boekelheide, Kim // PLoS ONE;2011, Vol. 6 Issue 6, p1 

    Background: In previous studies using candidate gene approaches, low sperm count (oligospermia) has been associated with altered sperm mRNA content and DNA methylation in both imprinted and non-imprinted genes. We performed a genome-wide analysis of sperm DNA methylation and mRNA content to test...

  • Gene profiling study of G3139- and Bcl-2-targeting siRNAs identifies a unique G3139 molecular signature. Anderson, E. M.; Miller, P.; Ilsley, D.; Marshall, W.; Khvorova, A.; Stein, C. A.; Benimetskaya, L. // Cancer Gene Therapy;Apr2006, Vol. 13 Issue 4, p406 

    G3139 is a phosphorothioate oligodeoxyribonucleotide that is targeted to the initiation codon region of the Bcl-2 mRNA, which downregulates Bcl-2 protein and mRNA expression via an antisense mechanism. In previous work, we have demonstrated that the phenotype observed in several prostate and...

  • Integrating heterogeneous genomic data to accurately identify disease subtypes. Xianwen Ren; Hua Fu; Qi Jin // BMC Medical Genomics;11/20/2015, Vol. 8, p1 

    Background: High-throughput biotechnologies have been widely used to characterize clinical samples from various perspectives e.g., epigenomics, genomics and transcriptomics. However, because of the heterogeneity of these technologies and their outputs, individual analysis of the various types of...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics