Screening candidate genes for mutations in patients with hypogonadotropic hypogonadism using custom genome resequencing microarrays

Ning Xu, Robert H. Podolsky, Pranav Chudgar, Lynn P. Chorich, Chunmei Liu, Paul G McDonough, Janet A. Warrington, Lawrence C Layman

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Objective: The purpose of this study was to determine the consistency of calling single nucleotide polymorphisms (SNPs) by custom genome resequencing microarrays compared with capillary DNA sequencing. Study design: Amplified genomic DNA from 23 patients with hypogonadotropic hypogonadism was hybridized to microarrays containing 30 kilobases of sequence from 6 different candidate genes. Capillary DNA sequencing was performed in 10 patients. Results: For 10 patients with ≥90% of bases called, 49 SNPs in 5 of 6 genes were identified. Of the 490 bases, 75 were ambiguous (read as "N"), and 415 were able to be called an A, C, G, or T. Of 415 called, 401 (96.6%) sequences were confirmed by DNA sequencing. All homozygotes (285/285) were called identically, while sequence from 89.2% (116/130) of heterozygotes agreed by both methods. The level of agreement between microarray calls and capillary DNA sequencing demonstrated substantial accuracy. Conclusion: Custom genome resequencing microarrays are highly consistent with capillary sequencing in calling individual bases in genomic DNA from patients with human disease.

Original languageEnglish (US)
Pages (from-to)1274-1282
Number of pages9
JournalAmerican Journal of Obstetrics and Gynecology
Volume192
Issue number4
DOIs
StatePublished - Jan 1 2005

Fingerprint

Hypogonadism
DNA Sequence Analysis
Genome
Mutation
Genes
Single Nucleotide Polymorphism
DNA
Homozygote
Heterozygote

Keywords

  • Custom genome resequencing microarray
  • Genomic chip
  • Idiopathic hypogonadotropic hypogonadism
  • Microarray

ASJC Scopus subject areas

  • Obstetrics and Gynecology

Cite this

Screening candidate genes for mutations in patients with hypogonadotropic hypogonadism using custom genome resequencing microarrays. / Xu, Ning; Podolsky, Robert H.; Chudgar, Pranav; Chorich, Lynn P.; Liu, Chunmei; McDonough, Paul G; Warrington, Janet A.; Layman, Lawrence C.

In: American Journal of Obstetrics and Gynecology, Vol. 192, No. 4, 01.01.2005, p. 1274-1282.

Research output: Contribution to journalArticle

Xu, Ning ; Podolsky, Robert H. ; Chudgar, Pranav ; Chorich, Lynn P. ; Liu, Chunmei ; McDonough, Paul G ; Warrington, Janet A. ; Layman, Lawrence C. / Screening candidate genes for mutations in patients with hypogonadotropic hypogonadism using custom genome resequencing microarrays. In: American Journal of Obstetrics and Gynecology. 2005 ; Vol. 192, No. 4. pp. 1274-1282.
@article{2af4586a77c545a6b4fc855e558b8ca2,
title = "Screening candidate genes for mutations in patients with hypogonadotropic hypogonadism using custom genome resequencing microarrays",
abstract = "Objective: The purpose of this study was to determine the consistency of calling single nucleotide polymorphisms (SNPs) by custom genome resequencing microarrays compared with capillary DNA sequencing. Study design: Amplified genomic DNA from 23 patients with hypogonadotropic hypogonadism was hybridized to microarrays containing 30 kilobases of sequence from 6 different candidate genes. Capillary DNA sequencing was performed in 10 patients. Results: For 10 patients with ≥90{\%} of bases called, 49 SNPs in 5 of 6 genes were identified. Of the 490 bases, 75 were ambiguous (read as {"}N{"}), and 415 were able to be called an A, C, G, or T. Of 415 called, 401 (96.6{\%}) sequences were confirmed by DNA sequencing. All homozygotes (285/285) were called identically, while sequence from 89.2{\%} (116/130) of heterozygotes agreed by both methods. The level of agreement between microarray calls and capillary DNA sequencing demonstrated substantial accuracy. Conclusion: Custom genome resequencing microarrays are highly consistent with capillary sequencing in calling individual bases in genomic DNA from patients with human disease.",
keywords = "Custom genome resequencing microarray, Genomic chip, Idiopathic hypogonadotropic hypogonadism, Microarray",
author = "Ning Xu and Podolsky, {Robert H.} and Pranav Chudgar and Chorich, {Lynn P.} and Chunmei Liu and McDonough, {Paul G} and Warrington, {Janet A.} and Layman, {Lawrence C}",
year = "2005",
month = "1",
day = "1",
doi = "10.1016/j.ajog.2004.12.066",
language = "English (US)",
volume = "192",
pages = "1274--1282",
journal = "American Journal of Obstetrics and Gynecology",
issn = "0002-9378",
publisher = "Mosby Inc.",
number = "4",

}

TY - JOUR

T1 - Screening candidate genes for mutations in patients with hypogonadotropic hypogonadism using custom genome resequencing microarrays

AU - Xu, Ning

AU - Podolsky, Robert H.

AU - Chudgar, Pranav

AU - Chorich, Lynn P.

AU - Liu, Chunmei

AU - McDonough, Paul G

AU - Warrington, Janet A.

AU - Layman, Lawrence C

PY - 2005/1/1

Y1 - 2005/1/1

N2 - Objective: The purpose of this study was to determine the consistency of calling single nucleotide polymorphisms (SNPs) by custom genome resequencing microarrays compared with capillary DNA sequencing. Study design: Amplified genomic DNA from 23 patients with hypogonadotropic hypogonadism was hybridized to microarrays containing 30 kilobases of sequence from 6 different candidate genes. Capillary DNA sequencing was performed in 10 patients. Results: For 10 patients with ≥90% of bases called, 49 SNPs in 5 of 6 genes were identified. Of the 490 bases, 75 were ambiguous (read as "N"), and 415 were able to be called an A, C, G, or T. Of 415 called, 401 (96.6%) sequences were confirmed by DNA sequencing. All homozygotes (285/285) were called identically, while sequence from 89.2% (116/130) of heterozygotes agreed by both methods. The level of agreement between microarray calls and capillary DNA sequencing demonstrated substantial accuracy. Conclusion: Custom genome resequencing microarrays are highly consistent with capillary sequencing in calling individual bases in genomic DNA from patients with human disease.

AB - Objective: The purpose of this study was to determine the consistency of calling single nucleotide polymorphisms (SNPs) by custom genome resequencing microarrays compared with capillary DNA sequencing. Study design: Amplified genomic DNA from 23 patients with hypogonadotropic hypogonadism was hybridized to microarrays containing 30 kilobases of sequence from 6 different candidate genes. Capillary DNA sequencing was performed in 10 patients. Results: For 10 patients with ≥90% of bases called, 49 SNPs in 5 of 6 genes were identified. Of the 490 bases, 75 were ambiguous (read as "N"), and 415 were able to be called an A, C, G, or T. Of 415 called, 401 (96.6%) sequences were confirmed by DNA sequencing. All homozygotes (285/285) were called identically, while sequence from 89.2% (116/130) of heterozygotes agreed by both methods. The level of agreement between microarray calls and capillary DNA sequencing demonstrated substantial accuracy. Conclusion: Custom genome resequencing microarrays are highly consistent with capillary sequencing in calling individual bases in genomic DNA from patients with human disease.

KW - Custom genome resequencing microarray

KW - Genomic chip

KW - Idiopathic hypogonadotropic hypogonadism

KW - Microarray

UR - http://www.scopus.com/inward/record.url?scp=16844362169&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=16844362169&partnerID=8YFLogxK

U2 - 10.1016/j.ajog.2004.12.066

DO - 10.1016/j.ajog.2004.12.066

M3 - Article

C2 - 15846219

AN - SCOPUS:16844362169

VL - 192

SP - 1274

EP - 1282

JO - American Journal of Obstetrics and Gynecology

JF - American Journal of Obstetrics and Gynecology

SN - 0002-9378

IS - 4

ER -