Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Affymetrix SNP and CNV data for the HuRef individual

ABSTRACT: The ideal genome sequence for medical interpretation is complete and diploid, capturing the full spectrum of genetic variation. Toward this end, there has been progress in discovery of single nucleotide polymorphism (SNP) and small (<10bp) insertion/deletions (indels), but annotation of larger structural variation (SV) including copy number variation (CNV) has been less comprehensive, even with available diploid sequence assemblies. We applied a multi-step sequence and microarray-based analysis to identify numerous previously unknown SVs within the first genome sequence reported from an individual. An Affymetrix SNP array experiment was performed according to the manufacturer's directions on DNA extracted from a lymphoblastoid cell line (HuRef). Copy number analysis of Affymetrix 6.0 SNP arrays was performed for the HuRef sample. The HuRef sample was run in a batch of 50 control samples, which were used as baseline for calling CNVs.

ORGANISM(S): Homo sapiens

SUBMITTER: Andy Pang

PROVIDER: E-GEOD-20275 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Towards a comprehensive structural variation map of an individual human genome.

Pang Andy W AW MacDonald Jeffrey R JR Pinto Dalila D Wei John J Rafiq Muhammad A MA Conrad Donald F DF Park Hansoo H Hurles Matthew E ME Lee Charles C Venter J Craig JC Kirkness Ewen F EF Levy Samuel S Feuk Lars L Scherer Stephen W SW

Genome biology 20100519 5

<h4>Background</h4>Several genomes have now been sequenced, with millions of genetic variants annotated. While significant progress has been made in mapping single nucleotide polymorphisms (SNPs) and small (<10 bp) insertion/deletions (indels), the annotation of larger structural variants has been less comprehensive. It is still unclear to what extent a typical genome differs from the reference assembly, and the analysis of the genomes sequenced to date have shown varying results for copy number ...[more]

PMID: 20482838

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Project description:Generating sufficient DNA for high-throughput genetic analysis has always been a challenge for clinical settings where the amount of source DNA is limited. Multiple displacement amplification (MDA) has been proposed as a promising candidate for such situations. Previous work with lower-resolution arrays confirmed the utility of single-cell MDA products for large-size (~30 Mb) genome variation screening. We tested the performance of single-cell MDA products on the SNP 6.0 arrays to examine the performance of single-cell MDA in SNP genotyping, copy number polymorphism, de novo copy number variation (CNV) and loss of heterozygosity (LOH) analysis. Our data show that for SNP genotyping, single-cell MDA did not obtain complete genome coverage or high sequence fidelity. For CNV calling, single-cell MDA introduced stochastic amplification artifacts in log2 ratio profiles, reducing the robustness of CNV calling; however, by adjusting smooth window size, it is still possible to analyze large chromosomal aberrations, and homozygous deletions as small as 500 kb can still be identified from the noisy log2 ratio profiles. Our results also suggest that even with a modified protocol (reduction of reaction volume, addition of a molecular crowding reagent, minimization of reaction time), single-cell MDA presented little improvement over the unmodified protocol, but by increasing the number of cells as template to 5M-bM-^@M-^S10 cells, SNP 6.0 array results comparable to those of 10 ng genomic DNA MDA could be obtained. Algorithms like PICNIC improved the CNV calling, suggesting that better algorithms can better utilize single-cell MDA array results. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cell line samples, and multiple displacement samples. Genotyping, Copy number and LOH analysis of Affymetrix SNP 6.0 arrays was performed for 3 samples of unamplified cell line genomic DNA, 2 samples of DNA obtained by multiple displacement amplification from 10ng genomic DNA, 3 single-cell multiple displacement amplification (MDA) products, single cell modified MDA amplification product, 5-cell modified MDA amplification product, 10-cell modified MDA amplification product.

Dataset Information

Affymetrix SNP and CNV data for the HuRef individual

Publications

Towards a comprehensive structural variation map of an individual human genome.

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