SEQUENOM MALDITOFMS Samples were genotyped at INRA on their Seqeunom MALDITOF mass spectrometer MALDITOFMS Matrix assisted laser desorbption ionisation time of flight mass spectrometry ID: 934200
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Slide1
Data Quality Control
Slide2Candidate Genes project
Slide3SEQUENOM MALDI-TOF-MS
Samples were genotyped at INRA on their
Seqeunom
MALDI-TOF mass spectrometer
Slide4MALDI-TOF-MS
Matrix assisted laser
desorbption
ionisation
– time of flight – mass spectrometry
Slide5Machine is calibrated with known samples and the time of flight (TOF) of the high mass allele is plotted against the TOF of the low mass allele.
We expect to see three groups corresponding to homozygous high mass allele, homozygous low mass allele and heterozygous in the middle.
The angles between these groups are calculated and suitable cutoffs are chosen that will accurately discriminate between groups.
This angle is shown in subsequent plots
Slide6Genotype #Samples
Homozygous ref : 364
Heterozygous 755
Homozygous alt: 390
Hardy Weinberg p = 1
IL4 rs2070874
Slide7Monomorphic SNP rs1136754 in HLAA
Monomorphic SNP should probably be excluded from the analysis for two reasons:
They are uninformative and so no association will be found with them.
Absence of alleles at a locus that is known to be polymorphic at high frequency, (we would not be testing it otherwise) might indicate a problem with the assay so the observation could be wrong and misleading.
My one reservation is that if the allele has been correctly called imputation might bring in a SNP that
is polymorphic
.
Slide8Clearly a problem with how this one has been scored.
Should be removed from analysis until problem resolved.
Slide9Genotype #Samples
Homozygous ref : 446
Heterozygous 113
Homozygous alt: 1103
Hardy Weinberg p = 1.642e-269
Clearly not in HWE but in HLA region which is often not in HWE
HLAG rs9380142
Slide10Hardy Weinberg p =0.06
Just in HWE but suspicious deficiency of Homozygote alternate alleles for this SNP in IFNG
Slide11Big cluster of uncalled samples.
What are they?
Could they cause a systematic bias?
Need to genotype some of the unclassified by another method if this NSP in MIF has association
Slide12PCA CLUSTERING