Nanopore sequencing as a novel method of characterising anorexia nervosa risk loci
Abstract Background Anorexia nervosa (AN) is a polygenic, severe metabopsychiatric disorder with poorly understood aetiology. Eight significant loci have been identified by genome-wide association studies (GWAS) and single nucleotide polymorphism (SNP)-based heritability was estimated to be ~ 11–17,...
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2024-12-01
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| Online Access: | https://doi.org/10.1186/s12864-024-11172-7 |
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| author | Natasha Berthold Silvana Gaudieri Sean Hood Monika Tschochner Allison L. Miller Jennifer Jordan Laura M. Thornton Cynthia M. Bulik Patrick Anthony Akkari Martin A. Kennedy |
| author_facet | Natasha Berthold Silvana Gaudieri Sean Hood Monika Tschochner Allison L. Miller Jennifer Jordan Laura M. Thornton Cynthia M. Bulik Patrick Anthony Akkari Martin A. Kennedy |
| author_sort | Natasha Berthold |
| collection | DOAJ |
| description | Abstract Background Anorexia nervosa (AN) is a polygenic, severe metabopsychiatric disorder with poorly understood aetiology. Eight significant loci have been identified by genome-wide association studies (GWAS) and single nucleotide polymorphism (SNP)-based heritability was estimated to be ~ 11–17, yet causal variants remain elusive. It is therefore important to define the full spectrum of genetic variants in the wider regions surrounding these significantly associated loci. The hypothesis we evaluate here is that unrecognised or relatively unexplored variants in these regions exist and are promising targets for future functional analyses. To test this hypothesis, we implemented a novel approach with targeted nanopore sequencing (Oxford Nanopore Technologies) for 200 kb regions centred on each of the eight AN-associated loci in 10 AN case samples. Our bioinformatics pipeline entailed base-calling and alignment with Dorado and minimap2 software, followed by variant calling with four separate tools, Sniffles2, Clair3, Straglr, and NanoVar. We then leveraged publicly available databases to characterise these loci in putative functional context and prioritise a subset of potentially relevant variants. Results Targeted nanopore sequencing effectively enriched the target regions (average coverage 14.64x). To test our hypothesis, we curated a list of 20 prioritised variants in non-coding regions, poorly represented in the current human reference genome but that may have functional consequences in AN pathology. Notably, we identified a polymorphic SINE-VNTR-Alu like sub-family D element (SVA-D), intergenic with IP6K2 and PRKAR2A, and a poly-T short tandem repeat (STR) in the 3ʹUTR of FOXP1. Conclusions Our results highlight the potential of targeted nanopore sequencing for characterising poorly resolved or complex variation, which may be initially obscured in risk-associated regions detected by GWAS. Some of the variants identified in this way, such as the polymorphic SVA-D and poly-T STR, could contribute to mechanisms of phenotypic risk, through regulation of several neighbouring genes implicated in AN biology, and affect post-transcriptional processing of FOXP1, respectively. This exploratory investigation was not powered to detect functional effects, however, the variants we observed using this method are poorly represented in the current human reference genome and accompanying databases, and further examination of these may provide new opportunities for improved understanding of genetic risk mechanisms of AN. |
| format | Article |
| id | doaj-art-19723cf4d16f4b3e8dd4afa13e9ed11c |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj-art-19723cf4d16f4b3e8dd4afa13e9ed11c2025-01-05T12:09:27ZengBMCBMC Genomics1471-21642024-12-0125111110.1186/s12864-024-11172-7Nanopore sequencing as a novel method of characterising anorexia nervosa risk lociNatasha Berthold0Silvana Gaudieri1Sean Hood2Monika Tschochner3Allison L. Miller4Jennifer Jordan5Laura M. Thornton6Cynthia M. Bulik7Patrick Anthony Akkari8Martin A. Kennedy9University of Western AustraliaUniversity of Western AustraliaUniversity of Western AustraliaUniversity of Notre Dame AustraliaPathology and Biomedical Science Department, University of Otago ChristchurchDepartment of Psychological Medicine, University of Otago ChristchurchDepartment of Psychiatry, University of North Carolina at Chapel HillDepartment of Psychiatry, University of North Carolina at Chapel HillUniversity of Western AustraliaPathology and Biomedical Science Department, University of Otago ChristchurchAbstract Background Anorexia nervosa (AN) is a polygenic, severe metabopsychiatric disorder with poorly understood aetiology. Eight significant loci have been identified by genome-wide association studies (GWAS) and single nucleotide polymorphism (SNP)-based heritability was estimated to be ~ 11–17, yet causal variants remain elusive. It is therefore important to define the full spectrum of genetic variants in the wider regions surrounding these significantly associated loci. The hypothesis we evaluate here is that unrecognised or relatively unexplored variants in these regions exist and are promising targets for future functional analyses. To test this hypothesis, we implemented a novel approach with targeted nanopore sequencing (Oxford Nanopore Technologies) for 200 kb regions centred on each of the eight AN-associated loci in 10 AN case samples. Our bioinformatics pipeline entailed base-calling and alignment with Dorado and minimap2 software, followed by variant calling with four separate tools, Sniffles2, Clair3, Straglr, and NanoVar. We then leveraged publicly available databases to characterise these loci in putative functional context and prioritise a subset of potentially relevant variants. Results Targeted nanopore sequencing effectively enriched the target regions (average coverage 14.64x). To test our hypothesis, we curated a list of 20 prioritised variants in non-coding regions, poorly represented in the current human reference genome but that may have functional consequences in AN pathology. Notably, we identified a polymorphic SINE-VNTR-Alu like sub-family D element (SVA-D), intergenic with IP6K2 and PRKAR2A, and a poly-T short tandem repeat (STR) in the 3ʹUTR of FOXP1. Conclusions Our results highlight the potential of targeted nanopore sequencing for characterising poorly resolved or complex variation, which may be initially obscured in risk-associated regions detected by GWAS. Some of the variants identified in this way, such as the polymorphic SVA-D and poly-T STR, could contribute to mechanisms of phenotypic risk, through regulation of several neighbouring genes implicated in AN biology, and affect post-transcriptional processing of FOXP1, respectively. This exploratory investigation was not powered to detect functional effects, however, the variants we observed using this method are poorly represented in the current human reference genome and accompanying databases, and further examination of these may provide new opportunities for improved understanding of genetic risk mechanisms of AN.https://doi.org/10.1186/s12864-024-11172-7Eating disordersPsychiatric geneticsAnorexia nervosa risk lociStructural variantsTransposable elementsNanopore sequencing |
| spellingShingle | Natasha Berthold Silvana Gaudieri Sean Hood Monika Tschochner Allison L. Miller Jennifer Jordan Laura M. Thornton Cynthia M. Bulik Patrick Anthony Akkari Martin A. Kennedy Nanopore sequencing as a novel method of characterising anorexia nervosa risk loci BMC Genomics Eating disorders Psychiatric genetics Anorexia nervosa risk loci Structural variants Transposable elements Nanopore sequencing |
| title | Nanopore sequencing as a novel method of characterising anorexia nervosa risk loci |
| title_full | Nanopore sequencing as a novel method of characterising anorexia nervosa risk loci |
| title_fullStr | Nanopore sequencing as a novel method of characterising anorexia nervosa risk loci |
| title_full_unstemmed | Nanopore sequencing as a novel method of characterising anorexia nervosa risk loci |
| title_short | Nanopore sequencing as a novel method of characterising anorexia nervosa risk loci |
| title_sort | nanopore sequencing as a novel method of characterising anorexia nervosa risk loci |
| topic | Eating disorders Psychiatric genetics Anorexia nervosa risk loci Structural variants Transposable elements Nanopore sequencing |
| url | https://doi.org/10.1186/s12864-024-11172-7 |
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