Accurate single-nucleotide polymorphism allele assignment in trisomic or duplicated regions by using a single base-extension assay with MALDI-TOF mass spectrometry

Trewick, Anne L., El-Sayed Moustafa, Julia S., De Smith, Adam J., Froguel, Philippe, Greve, Gottfried, Njolstad, Pal R., Coin, Lachlan J. M. and Blakemore, A.I.F. (2011) Accurate single-nucleotide polymorphism allele assignment in trisomic or duplicated regions by using a single base-extension assay with MALDI-TOF mass spectrometry. Clinical Chemistry, 57 8: 1188-1195. doi:10.1373/clinchem.2010.159558


Author Trewick, Anne L.
El-Sayed Moustafa, Julia S.
De Smith, Adam J.
Froguel, Philippe
Greve, Gottfried
Njolstad, Pal R.
Coin, Lachlan J. M.
Blakemore, A.I.F.
Title Accurate single-nucleotide polymorphism allele assignment in trisomic or duplicated regions by using a single base-extension assay with MALDI-TOF mass spectrometry
Journal name Clinical Chemistry   Check publisher's open access policy
ISSN 0009-9147
1530-8561
Publication date 2011-01-01
Year available 2011
Sub-type Article (original research)
DOI 10.1373/clinchem.2010.159558
Open Access Status Not Open Access
Volume 57
Issue 8
Start page 1188
End page 1195
Total pages 8
Place of publication Washington, DC United States
Publisher American Association for Clinical Chemistry, Inc.
Language eng
Subject 1308 Clinical Biochemistry
2704 Biochemistry, medical
Abstract BACKGROUND: The accurate assignment of alleles embedded within trisomic or duplicated regions is an essential prerequisite for assessing the combined effects of single-nucleotide polymorphisms (SNPs) and genomic copy number. Such an integrated analysis is challenging because heterozygotes for such a SNP may be one of 2 genotypes - AAB or ABB. Established methods for SNP genotyping, however, can have difficulty discriminating between the 2 heterozygous trisomic genotypes.Wedeveloped a method for assigning heterozygous trisomic genotypes that uses the ratio of the height of the 2 allele peaks obtained by mass spectrometry after a single-base extension assay. METHODS: Eighteen COL6A2 (collagen, type VI, alpha 2) SNPs were analyzed in euploid and trisomic individuals by means of a multiplexed single-base extension assay that generated allele-specific oligonucleotides of differing M r values for detection by MALDI-TOF mass spectrometry. Reference data (mean and SD) for the allele peak height ratios were determined from heterozygous euploid samples. The heterozygous trisomic genotypes were assigned by calculating the z score for each trisomic allele peak height ratio and by considering the sign (+/-) of the z score. RESULTS: Heterozygous trisomic genotypes were assigned in 96.1% (range, 89.9%-100%) of the samples for each SNP analyzed. The genotypes obtained were reproduced in 95 (97.5%) of 97 loci retested in a second assay. Subsequently, the origin of nondisjunction was determined in 108 (82%) of 132 family trios with a Down syndrome child. CONCLUSIONS: This approach enabled reliable genotyping of heterozygous trisomic samples and the determination of the origin of nondisjunction in Down syndrome family trios.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
 
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