Dataset Information

Performance assessment of copy number microarray platforms using a spike-in experiment.

ABSTRACT:

Motivation

Changes in the copy number of chromosomal DNA segments [copy number variants (CNVs)] have been implicated in human variation, heritable diseases and cancers. Microarray-based platforms are the current established technology of choice for studies reporting these discoveries and constitute the benchmark against which emergent sequence-based approaches will be evaluated. Research that depends on CNV analysis is rapidly increasing, and systematic platform assessments that distinguish strengths and weaknesses are needed to guide informed choice.

Results

We evaluated the sensitivity and specificity of six platforms, provided by four leading vendors, using a spike-in experiment. NimbleGen and Agilent platforms outperformed Illumina and Affymetrix in accuracy and precision of copy number dosage estimates. However, Illumina and Affymetrix algorithms that leverage single nucleotide polymorphism (SNP) information make up for this disadvantage and perform well at variant detection. Overall, the NimbleGen 2.1M platform outperformed others, but only with the use of an alternative data analysis pipeline to the one offered by the manufacturer.

Availability

The data is available from http://rafalab.jhsph.edu/cnvcomp/.

Contact

pevsner@jhmi.edu; fspencer@jhmi.edu; rafa@jhu.edu

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Halper-Stromberg E

PROVIDER: S-EPMC3072561 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Performance assessment of copy number microarray platforms using a spike-in experiment.

Halper-Stromberg Eitan E Frelin Laurence L Ruczinski Ingo I Scharpf Robert R Jie Chunfa C Carvalho Benilton B Hao Haiping H Hao Haiping H Hetrick Kurt K Jedlicka Anne A Dziedzic Amanda A Doheny Kim K Scott Alan F AF Baylin Steve S Pevsner Jonathan J Spencer Forrest F Irizarry Rafael A RA

Bioinformatics (Oxford, England) 20110401 8

<h4>Motivation</h4>Changes in the copy number of chromosomal DNA segments [copy number variants (CNVs)] have been implicated in human variation, heritable diseases and cancers. Microarray-based platforms are the current established technology of choice for studies reporting these discoveries and constitute the benchmark against which emergent sequence-based approaches will be evaluated. Research that depends on CNV analysis is rapidly increasing, and systematic platform assessments that distingu ...[more]

PMID: 21478196

Similar Datasets

Project description:BackgroundFetal echogenic bowel (FEB) is associated with an increased risk of poor pregnant outcomes; however, karyotyping fails to detect copy number variations (CNVs) in FEB. This study aimed to evaluate the performance of chromosomal microarray analysis (CMA) for detection of FEB.MethodsThe medical records of 147 pregnant women with FEB recruited during December 2015 to December 2018 were retrospectively reviewed, and prenatal samples were collected for karyotyping and CMA. The detection of chromosomal abnormality was compared between karyotyping and CMA.ResultsKaryotyping identified eight cases with abnormal karyotypes (5.44% prevalence), including four fetuses with pathogenic aneuploidy, three with chromosome polymorphism and one with balanced chromosome translocation. CMA identified 13 abnormal CNVs (8.84% prevalence), including 4 fetuses with pathogenic aneuploidy as detected by karyotyping and 9 additional CNVs with normal karyotypes; however, CMA failed to detect chromosome polymorphism and balanced chromosome translocation. In fetuses with isolated FEB, no cases presented pathogenic findings and CMA detected two cases with variants of uncertain significance (VOUS). In cases presenting FEB along with other ultrasound abnormalities, CMA detected three cases with pathogenic CNVs and four cases with VOUS in addition to four cases with aneuploidy. There was no significant difference in the detection of abnormal CNVs between the fetuses with echogenic bowel alone and along with other ultrasound abnormalities (10% vs 8.67%, P > 0.05). Except 9 fetuses lost to the follow-up, the other 138 fetuses with echogenic bowel were successfully followed up. Pregnancy was terminated in 5 fetuses with chromosomal abnormality, 2 with pathogenic CNVs and 1 with VOUS, and other 16 with normal karyotypes and CMA findings but showing ultrasound abnormalities or multiple malformations.ConclusionIsolated FEB is associated with a good prognosis, and a satisfactory pregnant outcome is expected for fetuses with echogenic bowel that are negative for chromosomal anomalies and other severe structure abnormalities. CMA shows an important value in the genetic diagnosis of FEB. As a supplement to karyotyping, CMA may improve the accuracy of prenatal diagnosis of fetal intestinal malformations in pregnant women with FEB.

Dataset Information

Performance assessment of copy number microarray platforms using a spike-in experiment.

Motivation

Results

Availability

Contact

Supplementary information

Publications

Performance assessment of copy number microarray platforms using a spike-in experiment.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets