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.
  
  
  METHODS
  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 > or =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.
  
  
  CONCLUSIONS
  Custom genome resequencing microarrays are highly consistent with capillary sequencing in calling individual bases in genomic DNA from patients with human disease.
authors.affiliation: Section of Reproductive Endocrinology, Infertility, and Genetics, Department of Obstetrics and Gynecology, The Medical College of Georgia, Augusta, GA 30912, USA.
authors.forename: Ning
authors.initials: N
authors.lastname: Xu
authors.forename: Robert H
authors.initials: RH
authors.lastname: Podolsky
authors.forename: Pranav
authors.initials: P
authors.lastname: Chudgar
authors.forename: Lynn P
authors.initials: LP
authors.lastname: Chorich
authors.forename: Chunmei
authors.initials: C
authors.lastname: Liu
authors.forename: Paul G
authors.initials: PG
authors.lastname: McDonough
authors.forename: Janet A
authors.initials: JA
authors.lastname: Warrington
authors.forename: Lawrence C
authors.initials: LC
authors.lastname: Layman
mesh_terms: D000293:Adolescent; D001483:Base Sequence; D015331:Cohort Studies; D005260:Female; D037201:Follicle Stimulating Hormone, beta Subunit / Q000235:genetics; D005820:Genetic Testing / Q000379:methods*; D015894:Genome, Human; D007987:Gonadotropin-Releasing Hormone / Q000235:genetics; D006065:Gonadotropins, Pituitary / Q000235:genetics* / Q000378:metabolism; D018398:Homeodomain Proteins / Q000235:genetics; D006801:Humans; D007006:Hypogonadism / Q000175:diagnosis / Q000235:genetics*; D008297:Male; D046228:Microarray Analysis; D008969:Molecular Sequence Data; D050809:POU Domain Factors; D017354:Point Mutation; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity; D014157:Transcription Factors / Q000235:genetics
chemical_list: D037201:Follicle Stimulating Hormone, beta Subunit; D006065:Gonadotropins, Pituitary; C489736:HESX1 protein, human; D018398:Homeodomain Proteins; C411985:NSMF protein, human; D050809:POU Domain Factors; D014157:Transcription Factors; C085076:transcription factor Brn-2; D007987:Gonadotropin-Releasing Hormone