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Table 1 Sample Characteristics.

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

Sample ID Group TISSUE ORIGIN Whole mtDNA SEQUENCING PREVIOUSLY PERFORMED COMPARATIVE SEQUENCING METHOD mtDNA Haplogroup MFP Predicted Haplogroup Unique or Pathogenic Known Feature Heteroplasmic variant levels MitoChip Detection of a priori known feature(s) MFP MitoChip v2.0 Call Rate (%)
1 Clinical Blood No Common point mutation panel (Baylor) H H None   Yes 99.5
2 Clinical Blood No Common point mutation panel (Baylor) I2 I Heteroplasmic 3243A > G 84% Yes 99.7
3 Clinical Blood No DHPLC (Transgenomics) B2b R* None   Yes 99.6
4 Clinical Blood No DHPLC (Transgenomics) R* R* None   Yes 99.5
5 Clinical Muscle No DHPLC (Transgenomics) N1b2 N1* None   Yes 99.7
6 Clinical Muscle Yes Sanger (Baylor) J1c J Homoplasmic 10845C > T Heteroplasmic 5049C > T Not reported Yes 99.8
7 Clinical Muscle& Yes Sanger (Baylor) J1c J Homoplasmic 12264C > T 100% Yes 99.6
8 Clinical Blood& No qPCR of heteroplasmic variant (Baylor) J1c J Heteroplasmic 12264C > T 30% Yes 99.6
9 Clinical Blood Yes Sanger (Baylor) N1a N1* Homoplasmic T insertion between 5537 and 5538   Yes 99.8
10 Clinical Blood Yes Sanger (Baylor) N1b2 N1* None   Yes 99.7
11 Clinical Blood Yes Sanger (Baylor) W1c W Homoplasmic 11204T > C   Yes 99.6
12 Clinical Blood Yes Sanger (Baylor) L1b1a L0/L1 Homoplasmic 11778G > A   Yes 99.5
13 Clinical Fibroblast Cell Line Yes Sanger (Baylor) H H None   Yes 99.6
14 Research Cell line Yes Sanger (MPK) K L3 5 Kb deletion   Yes N/A
15 Research Hela Cell Line Yes Illumina GAII (JAB) L3b1a1 L3 None   No 99.7
16 Research Blood Yes Sanger (TGS) V7 V None   Yes 99.7
17 Research Blood Yes Sanger (TGS) H11 H Heteroplasmy 9966G > A 20% No 98.5
18 Research Blood Yes Sanger (TGS) U4a U* Heteroplasmy 1706A > G 25% No 98.9
19 Research Blood Yes Sanger (TGS) D5a L3 None   Yes 99.7
20 Research Blood Yes Sanger (TGS) D5a L3 None   Yes 99.6
21 Research Blood Yes Sanger (TGS) J1c2 J Heteroplasmy 12879C > T 45% Yes 99.7
22 Research Blood Yes Sanger (TGS) T1a T None   Yes 99.6
23 Research Blood Yes Sanger (TGS) U4b3 U* None   Yes 99.8
24 Research Blood Yes Sanger (TGS) D5c L3 None   Yes 99.6
  1. 13 clinical samples and 11 research samples were analyzed by MitoChip v2.0. Tissue origin, comparative mtDNA genome sequencing methodologies, unique or pathogenic features that characterize particular samples based on a priori sequencing knowledge, variant heteroplasmy levels, as well as MitoChip performance in terms of ability to detect known variants and the call rate achieved using MitoChip Filtering Protocol (MFP) are detailed. The 'mtDNA haplogroup' column details the manually curated haplogroup based on full sequence analysis for each sample. 'MitoSNP predicted haplogroup' was based on a subset of 22 mtDNA positions and generally agreed with manual curation, with the exception of haplogroups B, K, and D that were not properly identified by MitoSNP prediction. &, muscle and blood samples originated from the same subject.