Clinical utility of whole genome sequencing for the detection of mitochondrial genome mutations

1.
Division of Human Genetics, Children's Hospital Medical Center, Cincinnati, OH 45229, USA
2.
Division of Human Genetics, Children's Hospital Medical Center, Cincinnati, OH 45229, USA
3.
PerkinElmer Genomics, Branford, CT 06405, USA
4.
Aperiomics, Inc., Sterling, VA 20166, USA
5.
Lake Erie College of Osteopathic Medicine, Erie, PA 16509, USA
6.
Division of Human Genetics, Children's Hospital Medical Center, Cincinnati, OH 45229, USA

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Corresponding author: E-mail address: taosheng.huang@cchmc.org (Taosheng Huang)

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Table 1. Comparison of variant calls and discordant variants between WGS and PCR-NGS datasets when analyzed by the WGS pipeline.

Sample ID	Number of variants called by PCR-NGS	Number of variants called by WGS	Known pathogenic variants	Heteroplasmy level for known pathogenic variants – PCR-NGS (%)	Heteroplasmy level for known pathogenic variants – WGS (%)	Concordance rate (%)	Number of discordant variant	Interpretation of discordant variant
Sample 1	41	41	m.3243A>G	28	26	100	0	–
Sample 2	23	23	∗m.8696_15438del	99	40	100	0	–
Sample 3	31	30	m.8344A>G	96	93	97	1 (Fig.S3 A)	Alignment artifact from polynucleotide run
Sample 4	30	29	–	–	–	97	1 (Fig.S3 B)	Alignment artifact from polynucleotide run
Sample 5	76	77	m.8483_13446del	10	41	99	1 (Fig.S3 C)	m.11467A>G detected at 12% heteroplasmy level by WGS, but not detected at all by PCR-NGS. WGS call is likely an artifact
Sample 6	57	57	m.13513G>A	64	61	100	0	–
Sample 7	14	14	m.10382_15406del	98	20	100	0	–
Sample 8	15	15	m.3243A>G	13	14	100	0	–
Sample 9	20	20	m.10197G>A	54	49	100	0	–
Sample 10	97	98	m.8344A>G	92	80	99	1 (Fig.S3 D)	m.961T>G detected at 9% heteroplasmy level by WGS, but not detected at all by PCR-NGS. WGS call is likely an artifact
Sample 11	44	44	m.3243A>G	70	67	100	0	–
Sample 12	15	15	m.3243A>G	68	66	100	0	–
Sample 13	15	15	m.3243A>G	65	64	100	0	–
Heteroplasmy levels of point mutations and deletions in mtDNA of patients with clinical features of mitochondriopathy were identified by PCR-NGS and WGS. In the case of the three patients carrying mtDNA deletions (Samples 2, 5, and 7), there is an absence of other disease-causing variants in the nuclear or mitochondrial genomes; thus, their mtDNA deletions have been provisionally treated as the likely source of their mitochondriopathy. These deletions are also treated as a single variant for the purposes of counting the number of variant calls. Snapshots of each discordant variant position can be found in the indicated panels in Fig. S3. No insertions were observed in this set of patients by either PCR-NGS or WGS. It should also be noted that the region covered by the m.8696_15438del deletion in Sample 2 (indicated with an asterisk) also contains the pathogenic variant m.9957T > C, which is present at 100% and 97% frequency in PCR-NGS and WGS, respectively.

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Sample ID	Number of variants called by PCR-NGS	Number of variants called by WGS	Known pathogenic variants	Heteroplasmy level for known pathogenic variants – PCR-NGS (%)	Heteroplasmy level for known pathogenic variants – WGS (%)	Concordance rate (%)	Number of discordant variant	Interpretation of discordant variant
Sample 1	41	41	m.3243A>G	28	26	100	0	–
Sample 2	23	23	∗m.8696_15438del	99	40	100	0	–
Sample 3	31	30	m.8344A>G	96	93	97	1 (Fig.S3 A)	Alignment artifact from polynucleotide run
Sample 4	30	29	–	–	–	97	1 (Fig.S3 B)	Alignment artifact from polynucleotide run
Sample 5	76	77	m.8483_13446del	10	41	99	1 (Fig.S3 C)	m.11467A>G detected at 12% heteroplasmy level by WGS, but not detected at all by PCR-NGS. WGS call is likely an artifact
Sample 6	57	57	m.13513G>A	64	61	100	0	–
Sample 7	14	14	m.10382_15406del	98	20	100	0	–
Sample 8	15	15	m.3243A>G	13	14	100	0	–
Sample 9	20	20	m.10197G>A	54	49	100	0	–
Sample 10	97	98	m.8344A>G	92	80	99	1 (Fig.S3 D)	m.961T>G detected at 9% heteroplasmy level by WGS, but not detected at all by PCR-NGS. WGS call is likely an artifact
Sample 11	44	44	m.3243A>G	70	67	100	0	–
Sample 12	15	15	m.3243A>G	68	66	100	0	–
Sample 13	15	15	m.3243A>G	65	64	100	0	–
Heteroplasmy levels of point mutations and deletions in mtDNA of patients with clinical features of mitochondriopathy were identified by PCR-NGS and WGS. In the case of the three patients carrying mtDNA deletions (Samples 2, 5, and 7), there is an absence of other disease-causing variants in the nuclear or mitochondrial genomes; thus, their mtDNA deletions have been provisionally treated as the likely source of their mitochondriopathy. These deletions are also treated as a single variant for the purposes of counting the number of variant calls. Snapshots of each discordant variant position can be found in the indicated panels in Fig. S3. No insertions were observed in this set of patients by either PCR-NGS or WGS. It should also be noted that the region covered by the m.8696_15438del deletion in Sample 2 (indicated with an asterisk) also contains the pathogenic variant m.9957T > C, which is present at 100% and 97% frequency in PCR-NGS and WGS, respectively.

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doi: 10.1016/j.jgg.2020.03.001

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Clinical utility of whole genome sequencing for the detection of mitochondrial genome mutations

Corresponding author: E-mail address: taosheng.huang@cchmc.org (Taosheng Huang)

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doi: 10.1016/j.jgg.2020.03.001

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Clinical utility of whole genome sequencing for the detection of mitochondrial genome mutations

Corresponding author: E-mail address: taosheng.huang@cchmc.org (Taosheng Huang)

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