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 language | English (US) |
|---|---|
| Pages (from-to) | 1274-1282 |
| Number of pages | 9 |
| Journal | American Journal of Obstetrics and Gynecology |
| Volume | 192 |
| Issue number | 4 |
| DOIs | |
| State | Published - Jan 1 2005 |
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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 journal › Article
}
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
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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 -