Mutation scanning by meltMADGE: validations using BRCA1 and LDLR, and demonstration of the potential to identify severe, moderate, silent, rare, and paucimorphic mutations in the general population.
We have developed a mutation-scanning approach suitable for whole population screening for unknown mutations. The method, meltMADGE, combines thermal ramp electrophoresis with MADGE to achieve suitable cost efficiency and throughput. The sensitivity was tested in blind trials using 54 amplicons representing the BRCA1 coding region and a panel of 94 unrelated family breast cancer risk consultands previously screened in a clinical diagnostic laboratory. All 10 common polymorphisms, 15/15 previously identified disease-causing mutations, and three previously untested single base changes were identified. Assays of LDLR exons 3 and 8 were validated in 460 familial hypercholesteremics and detected 8/9 known variants. We then applied the exon 3 assay in several DNA banks representing approximately 8000 subjects with known cholesterol values and applied both assays in one DNA bank (n = 3600). In exon 3 we identified one previously reported moderate mutation, P84S (n = 1), also associated with moderate hypercholesteremia in this subject; an unreported silent variant, N76N (n = 1); and known severe hypercholesteremia splice mutation 313+1G-->A (n = 2). Around exon 8 we identified a paucimorphism (n = 35) at the splice site 1061-8T-->C (known to be in complete linkage disequilibrium with T705I) and unreported sequence variants 1186+11G-->A (n = 1) and D335N G-->A (n = 1). The cholesterol value for D335N was on the 96.2 percentile and for T705I, 2/35 carriers were above the 99th percentile. Thus, variants with predicted severe, moderate, and no effect were identified at the population level. In contrast with case collections, CpG mutations predominated. MeltMADGE will enable definition of the full population spectrum of rare, paucimorphic, severe, moderate (forme fruste), and silent mutations and effects.
Alharbi
Khalid K
KK
Human Genetics Division, School of Medicine, University of Southampton, Southampton University Hospitals NHS Trust, Southampton SO16 6YD, United Kingdom.
Aldahmesh
Mohammed A
MA
Spanakis
Emmanuel
E
Haddad
Lema
L
Whittall
Roslyn A
RA
Chen
Xiao-he
XH
Rassoulian
Hamid
H
Smith
Matt J
MJ
Sillibourne
Julie
J
Ball
Nicola J
NJ
Graham
Nikki J
NJ
Briggs
Patricia J
PJ
Simpson
Iain A
IA
Phillips
David I W
DI
Lawlor
Deborah A
DA
Ye
Shu
S
Humphries
Stephen E
SE
Cooper
Cyrus
C
Smith
George Davey
GD
Ebrahim
Shah
S
Eccles
Diana M
DM
Day
Ian N M
IN
D001943:Breast Neoplasms / Q000235:genetics; D004252:DNA Mutational Analysis / Q000379:methods*; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods; D005260:Female; D019398:Genes, BRCA1; D006801:Humans; D006938:Hyperlipoproteinemia Type II / Q000235:genetics; D008297:Male; D009154:Mutation; D011110:Polymorphism, Genetic; D011159:Population Surveillance; D011973:Receptors, LDL / Q000235:genetics; D012680:Sensitivity and Specificity
D011973:Receptors, LDL