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Design and validation of a metabolic disorder resequencing microarray (BRUM1)
Author(s) -
Bruce Christopher K.,
Smith Matthew,
Rahman Fatima,
Liu Zhifeng,
McMullan Dominic J.,
Ball Sarah,
Hartley Jane,
Kroos Marian A.,
Heptinstall Lesley,
Reuser Arnold J.J.,
Rolfs Arndt,
Hendriksz Chris,
Kelly Deirdre A.,
Barrett Timothy G.,
MacDonald Fiona,
Maher Eamonn R.,
Gissen Paul
Publication year - 2010
Publication title -
human mutation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 162
eISSN - 1098-1004
pISSN - 1059-7794
DOI - 10.1002/humu.21261
Subject(s) - indel , biology , genetics , locus (genetics) , gene , point mutation , computational biology , copy number variation , microarray , mutation , bioinformatics , genotype , single nucleotide polymorphism , genome , gene expression
The molecular genetic diagnosis of inherited metabolic disorders is challenging. The diseases are rare, and most show locus heterogeneity. Hence, testing of the genes associated with IMDs is time consuming and often not easily available. We report a resequencing array that allows the simultaneous resequencing of up to 92 genes associated with IMDs. To validate the array, DNA samples from 51 patients with 52 different known variants (including point variants, small insertion, and deletions [indels]) in seven genes ( C14ORF133, GAA, NPC1, NPC2, VPS33B, WFS1 , and SLC19A2 ) were amplified by PCR and hybridized to the array. A further patient cohort with 48 different mutations in NPC1 were analyzed blind. Out of 76 point variants, 73 were identified using automated software analysis followed by manual review. Ten insertion and deletion variants were detected in the extra tiling using mutation specific probes, with 11 heterozygous deletions and 3 heterozygous insertions. In summary, we identified 96% (95% confidence interval [CI] 89–99%) of point variants added to the array, but the pickup rate reduced to 83% (95% CI 75–89%) when insertions/deletions were included. Although the methodology has strengths and weaknesses, application of this technique could expedite diagnosis in most patients with multilocus IMDs. Hum Mutat 31:1–8, 2010. © 2010 Wiley‐Liss, Inc.