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 yet assessed
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.
Keyword Medical Laboratory Technology
Medical Laboratory Technology
MEDICAL LABORATORY TECHNOLOGY
Q-Index Code C1
Q-Index Status Provisional Code
Grant ID 08/0003775
Institutional Status Non-UQ

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