Design and validation of a metabolic disorder resequencing microarray (BRUM1).
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.
Bruce
Christopher K
CK
School of Clinical and Experimental Medicine, The University of Birmingham, Birmingham, United Kingdom.
Smith
Matthew
M
Rahman
Fatima
F
Liu
Zhi-feng
ZF
McMullan
Dominic J
DJ
Ball
Sarah
S
Hartley
Jane
J
Kroos
Marian A
MA
Heptinstall
Lesley
L
Reuser
Arnold J J
AJ
Rolfs
Arndt
A
Hendriksz
Chris
C
Kelly
Deirdre A
DA
Barrett
Timothy G
TG
MacDonald
Fiona
F
Maher
Eamonn R
ER
Gissen
Paul
P
D002352:Carrier Proteins / Q000235:genetics; D020022:Genetic Predisposition to Disease; D006023:Glycoproteins / Q000235:genetics; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins; D008562:Membrane Glycoproteins / Q000235:genetics; D008565:Membrane Proteins / Q000235:genetics; D026901:Membrane Transport Proteins / Q000235:genetics; D008659:Metabolic Diseases / Q000175:diagnosis / Q000235:genetics*; D009154:Mutation; D000077296:Niemann-Pick C1 Protein; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results; D012107:Research Design; D017422:Sequence Analysis, DNA / Q000379:methods*; D033921:Vesicular Transport Proteins / Q000235:genetics; D000520:alpha-Glucosidases / Q000235:genetics
D002352:Carrier Proteins; D006023:Glycoproteins; D047908:Intracellular Signaling Peptides and Proteins; D008562:Membrane Glycoproteins; D008565:Membrane Proteins; D026901:Membrane Transport Proteins; C106881:NPC1 protein, human; C104585:NPC2 protein, human; D000077296:Niemann-Pick C1 Protein; C120043:SLC19A2 protein, human; C539711:VIPAS39 protein, human; C411584:VPS33B protein, human; D033921:Vesicular Transport Proteins; C114987:wolframin protein; C509951:GAA protein, human; D000520:alpha-Glucosidases