NUMT Confounding Biases Mitochondrial Heteroplasmy Calls in Favor of the Reference Allele
Homology between mitochondrial DNA (mtDNA) and nuclear DNA of mitochondrial origin (nuMTs) causes confounding when aligning short sequence reads to the reference human genome, as the true sequence origin cannot be determined. Using a systematic in silico approach, we here report the impact of all po...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-09-01
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| Series: | Frontiers in Cell and Developmental Biology |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fcell.2019.00201/full |
| _version_ | 1818327624367210496 |
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| author | Hannah Maude Hannah Maude Mira Davidson Natalie Charitakis Leo Diaz William H. T. Bowers Eva Gradovich Toby Andrew Derek Huntley |
| author_facet | Hannah Maude Hannah Maude Mira Davidson Natalie Charitakis Leo Diaz William H. T. Bowers Eva Gradovich Toby Andrew Derek Huntley |
| author_sort | Hannah Maude |
| collection | DOAJ |
| description | Homology between mitochondrial DNA (mtDNA) and nuclear DNA of mitochondrial origin (nuMTs) causes confounding when aligning short sequence reads to the reference human genome, as the true sequence origin cannot be determined. Using a systematic in silico approach, we here report the impact of all potential mitochondrial variants on alignment accuracy and variant calling. A total of 49,707 possible mutations were introduced across the 16,569 bp reference mitochondrial genome (16,569 × 3 alternative alleles), one variant at-at-time. The resulting in silico fragmentation and alignment to the entire reference genome (GRCh38) revealed preferential mapping of mutated mitochondrial fragments to nuclear loci, as variants increased loci similarity to nuMTs, for a total of 807, 362, and 41 variants at 333, 144, and 27 positions when using 100, 150, and 300 bp single-end fragments. We subsequently modeled these affected variants at 50% heteroplasmy and carried out variant calling, observing bias in the reported allele frequencies in favor of the reference allele. Four variants (chrM:6023A, chrM:4456T, chrM:5147A, and chrM:7521A) including a possible hypertension factor, chrM:4456T, caused 100% loss of coverage at the mutated position (with all 100 bp single-end fragments aligning to homologous, nuclear positions instead of chrM), rendering these variants undetectable when aligning to the entire reference genome. Furthermore, four mitochondrial variants reported to be pathogenic were found to cause significant loss of coverage and select haplogroup-defining SNPs were shown to exacerbate the loss of coverage caused by surrounding variants. Increased fragment length and use of paired-end reads both improved alignment accuracy. |
| first_indexed | 2024-12-13T12:19:14Z |
| format | Article |
| id | doaj.art-fb8839994eed4f119d8981c64a7487ce |
| institution | Directory Open Access Journal |
| issn | 2296-634X |
| language | English |
| last_indexed | 2024-12-13T12:19:14Z |
| publishDate | 2019-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Cell and Developmental Biology |
| spelling | doaj.art-fb8839994eed4f119d8981c64a7487ce2022-12-21T23:46:37ZengFrontiers Media S.A.Frontiers in Cell and Developmental Biology2296-634X2019-09-01710.3389/fcell.2019.00201467769NUMT Confounding Biases Mitochondrial Heteroplasmy Calls in Favor of the Reference AlleleHannah Maude0Hannah Maude1Mira Davidson2Natalie Charitakis3Leo Diaz4William H. T. Bowers5Eva Gradovich6Toby Andrew7Derek Huntley8Department of Life Sciences, Imperial College London, London, United KingdomSection of Genomics of Common Disease, Imperial College London, London, United KingdomDepartment of Life Sciences, Imperial College London, London, United KingdomDepartment of Life Sciences, Imperial College London, London, United KingdomDepartment of Life Sciences, Imperial College London, London, United KingdomDepartment of Life Sciences, Imperial College London, London, United KingdomDepartment of Life Sciences, Imperial College London, London, United KingdomSection of Genomics of Common Disease, Imperial College London, London, United KingdomDepartment of Life Sciences, Imperial College London, London, United KingdomHomology between mitochondrial DNA (mtDNA) and nuclear DNA of mitochondrial origin (nuMTs) causes confounding when aligning short sequence reads to the reference human genome, as the true sequence origin cannot be determined. Using a systematic in silico approach, we here report the impact of all potential mitochondrial variants on alignment accuracy and variant calling. A total of 49,707 possible mutations were introduced across the 16,569 bp reference mitochondrial genome (16,569 × 3 alternative alleles), one variant at-at-time. The resulting in silico fragmentation and alignment to the entire reference genome (GRCh38) revealed preferential mapping of mutated mitochondrial fragments to nuclear loci, as variants increased loci similarity to nuMTs, for a total of 807, 362, and 41 variants at 333, 144, and 27 positions when using 100, 150, and 300 bp single-end fragments. We subsequently modeled these affected variants at 50% heteroplasmy and carried out variant calling, observing bias in the reported allele frequencies in favor of the reference allele. Four variants (chrM:6023A, chrM:4456T, chrM:5147A, and chrM:7521A) including a possible hypertension factor, chrM:4456T, caused 100% loss of coverage at the mutated position (with all 100 bp single-end fragments aligning to homologous, nuclear positions instead of chrM), rendering these variants undetectable when aligning to the entire reference genome. Furthermore, four mitochondrial variants reported to be pathogenic were found to cause significant loss of coverage and select haplogroup-defining SNPs were shown to exacerbate the loss of coverage caused by surrounding variants. Increased fragment length and use of paired-end reads both improved alignment accuracy.https://www.frontiersin.org/article/10.3389/fcell.2019.00201/fullnuMTmtDNAgenotypemitochondrial variantsmitochondrial genotypeNGS |
| spellingShingle | Hannah Maude Hannah Maude Mira Davidson Natalie Charitakis Leo Diaz William H. T. Bowers Eva Gradovich Toby Andrew Derek Huntley NUMT Confounding Biases Mitochondrial Heteroplasmy Calls in Favor of the Reference Allele Frontiers in Cell and Developmental Biology nuMT mtDNA genotype mitochondrial variants mitochondrial genotype NGS |
| title | NUMT Confounding Biases Mitochondrial Heteroplasmy Calls in Favor of the Reference Allele |
| title_full | NUMT Confounding Biases Mitochondrial Heteroplasmy Calls in Favor of the Reference Allele |
| title_fullStr | NUMT Confounding Biases Mitochondrial Heteroplasmy Calls in Favor of the Reference Allele |
| title_full_unstemmed | NUMT Confounding Biases Mitochondrial Heteroplasmy Calls in Favor of the Reference Allele |
| title_short | NUMT Confounding Biases Mitochondrial Heteroplasmy Calls in Favor of the Reference Allele |
| title_sort | numt confounding biases mitochondrial heteroplasmy calls in favor of the reference allele |
| topic | nuMT mtDNA genotype mitochondrial variants mitochondrial genotype NGS |
| url | https://www.frontiersin.org/article/10.3389/fcell.2019.00201/full |
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