Mitochondrial genome sequence analysis: A custom bioinformatics pipeline substantially improves Affymetrix MitoChip v2.0 call rate and accuracy

Table 3 Heteroplasmy detection levels made using the MFP analysis algorithm.

Sample ID	mtDNA Genome Position	Heteroplasmy Level Sanger	Heteroplasmy Level MFP
2	A3243G	84%	61%
6	C5049T	N.D.	34%
8	C12264T	30%	43%
9	5537	5537_5538 insT (100%)	58%
	5538		45%
17	G9966A	20%	Sample excluded
18	A1709G	25%	Sample excluded
21	C12879T	45%	55%

Sample #2, #6, #8, and #21 had heteroplasmic variants detected both by Sanger sequencing and MFP analysis of MitoChip v2.0 data. Of interest, the 5537_5538insT in tRNA-TRP identified by Sanger sequencing in sample #9 was interpreted in MFP as a heteroplasmic mutation at both positions 5537 and 5538. Although a heteroplasmic A1709G site was detected by Sanger sequencing in sample #18, this sample was excluded from MFP analysis due to poor sample quality. "N.D." = not determined.

ISSN: 1471-2105