Analysis of Brugada syndrome loci reveals that fine-mapping clustered GWAS hits enhances the annotation of disease-relevant variants

Pinsach-Abuin, Mel·lina; Olmo, Bernat del; Pérez-Agustin, Adrian; Mates, Jesus; Allegue, Catarina; Iglesias, Anna; Ma, Qi; Merkurjev, Daria; Konovalov, Sergiy; Zhang, Jing; Sheikh, F. S. El; Telenti, Amalio; Brugada, Josép; Brugada, Ramón; Gymrek, Melissa; Iulio, Julia di; García-Bassets, Ivan; Pagans, Sara

doi:10.1016/j.xcrm.2021.100250

Cited by 7 publications

(17 citation statements)

References 111 publications

(229 reference statements)

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“…We have observed that the twenty-two heterozygous sites are split by major and minor allele frequencies, with all major alleles in one chromosomal copy and all minor alleles in the other chromosomal copy. This finding builds upon the previously proposed model that the 13 kb Hap1/Hap3 region represents Ying-Yang haplotypes 44 . To generate SCN10A amplicons, genomic DNA was extracted with the same modified salting-out method used to isolate the ∼20 kb T1-T4 targets ( Fig.…”

Section: Resultssupporting

confidence: 87%

“…Fig. 6B ) 44 . Intriguingly, we observed a slight haplotype bias in our tests with blood-derived samples (Hap1>Hap3), which we did not observe when amplifying the 13 kb fragment from HG001 (compare allele burden plots between Suppl.…”

Section: Resultsmentioning

confidence: 94%

“…We used the GIAB reference HG001/NA12878 as a source of genomic DNA to amplify the subset of SCN10A targets. WGS linked-read data 24,32 reveals that HG001 is a Hap1/Hap3 carrier in the SCN5A - SCN10A locus (TACCATT and CGGGGGC) 44 . WGS linked-read data 24,32 also reveals that HG001 carries another subset of fifteen heterozygous sites, some of which have also been recently associated with heart arrhythmia 42 .…”

Section: Resultsmentioning

confidence: 99%

“…We next benchmarked targeted TELL-Seq with previously generated ONT data of 13 kb SCN10A products amplified from peripheral blood-derived genomic DNA from three Hap1/Hap3 carriers (referred here to as individuals #1-3) 44 . Our results agreed with the previously reported genotypes in individuals #1 and #2, correctly recalling and phasing the 14 (7+7) clinically relevant heterozygous positions in these samples ( Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Amplicons from three unrelated individuals were previously generated from peripheral blood-derived genomic DNA 44 . Briefly, blood was collected in EDTA anti-coagulant BD Vacutainer tubes and genomic DNA was extracted using the Chemagic MSM I Instrument (PerkinElmer) following the manufacturer’s recommendations and stored at −20°C before PCR 44 .…”

Section: Methodsmentioning

confidence: 99%

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Targeted Phasing of 2-200 Kilobase DNA Fragments with a Short-Read Sequencer and a Single-Tube Linked-Read Library Method

Mikhaylova¹,

Rzepka²,

Kawamura³

et al. 2023

Preprint

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In the human genome, heterozygous sites are genomic positions with different alleles inherited from each parent. On average, there is a heterozygous site every 1-2 kilobases (kb). Resolving whether two alleles in neighboring heterozygous positions are physically linked—that is, phased—is possible with a short-read sequencer if the sequencing library captures long-range information. TELL-Seq is a library preparation method based on millions of barcoded micro-sized beads that enables instrument-free phasing of a whole human genome in a single PCR tube. TELL-Seq incorporates a unique molecular identifier (barcode) to the short reads generated from the same high-molecular-weight (HMW) DNA fragment (known as ‘linked-reads’). However, genome-scale TELL-Seq is not cost-effective for applications focusing on a single locus or a few loci. Here, we present an optimized TELL-Seq protocol that enables the cost-effective phasing of enriched loci (targets) of varying sizes, purity levels, and heterozygosity. Targeted TELL-Seq maximizes linked-read efficiency and library yield while minimizing input requirements, fragment collisions on microbeads, and sequencing burden. To validate the targeted protocol, we phased seven 180-200 kb loci enriched by CRISPR/Cas9-mediated excision coupled with pulse-field electrophoresis, four 20 kb loci enriched by CRISPR/Cas9-mediated protection from exonuclease digestion, and six 2-13 kb loci amplified by PCR. The selected targets have clinical and research relevance (BRCA1, BRCA2, MLH1, MSH2, MSH6, APC, PMS2, SCN5A-SCN10A, andPKI3CA). These analyses reveal that targeted TELL-Seq provides a reliable way of phasing allelic variants within targets (2-200 kb in length) with the low cost and high accuracy of short-read sequencing.

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Section: Resultssupporting

confidence: 87%

Section: Resultsmentioning

confidence: 94%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 3 more Smart Citations

Targeted Phasing of 2-200 Kilobase DNA Fragments with a Short-Read Sequencer and a Single-Tube Linked-Read Library Method

Mikhaylova¹,

Rzepka²,

Kawamura³

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

Targeted phasing of 2–200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method

Mikhaylova,

Rzepka,

Kawamura

et al. 2024

Sci Rep

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In the human genome, heterozygous sites refer to genomic positions with a different allele or nucleotide variant on the maternal and paternal chromosomes. Resolving these allelic differences by chromosomal copy, also known as phasing, is achievable on a short-read sequencer when using a library preparation method that captures long-range genomic information. TELL-Seq is a library preparation that captures long-range genomic information with the aid of molecular identifiers (barcodes). The same barcode is used to tag the reads derived from the same long DNA fragment within a range of up to 200 kilobases (kb), generating linked-reads. This strategy can be used to phase an entire genome. Here, we introduce a TELL-Seq protocol developed for targeted applications, enabling the phasing of enriched loci of varying sizes, purity levels, and heterozygosity. To validate this protocol, we phased 2–200 kb loci enriched with different methods: CRISPR/Cas9-mediated excision coupled with pulse-field electrophoresis for the longest fragments, CRISPR/Cas9-mediated protection from exonuclease digestion for mid-size fragments, and long PCR for the shortest fragments. All selected loci have known clinical relevance: BRCA1, BRCA2, MLH1, MSH2, MSH6, APC, PMS2, SCN5A-SCN10A, and PKI3CA. Collectively, the analyses show that TELL-Seq can accurately phase 2–200 kb targets using a short-read sequencer.

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Deciphering the tissue-specific functional effect of Alzheimer risk SNPs with deep genome annotation

Varathan,

Xie,

et al. 2023

Preprint

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Alzheimers disease (AD) is a highly heritable brain dementia, along with substantial failure of cognitive function. Large-scale genome-wide association studies (GWAS) have led to a significant set of SNPs associated with AD and related traits. GWAS hits usually emerge as clusters where a lead SNP with the highest significance is surrounded by other less significant neighboring SNPs. Although functionality is not guaranteed with even the strongest associations in the GWAS, the lead SNPs have been historically the focus of the field, with the remaining associations inferred as redundant. Recent deep genome annotation tools enable the prediction of function from a segment of DNA sequence with significantly improved precision, which allows in-silico mutagenesis to interrogate the functional effect of SNP alleles. In this project, we explored the impact of top AD GWAS hits on the chromatin functions, and whether it will be altered by the genomic context (i.e., alleles of neighborhood SNPs). Our results showed that highly correlated SNPs in the same LD block could have distinct impact on the downstream functions. Although some GWAS lead SNPs showed dominating functional effect regardless of the neighborhood SNP alleles, several other ones do get enhanced loss or gain of function under certain genomic context, suggesting potential extra information hidden in the LD blocks.

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Analysis of Brugada syndrome loci reveals that fine-mapping clustered GWAS hits enhances the annotation of disease-relevant variants

Cited by 7 publications

References 111 publications

Targeted Phasing of 2-200 Kilobase DNA Fragments with a Short-Read Sequencer and a Single-Tube Linked-Read Library Method

Targeted Phasing of 2-200 Kilobase DNA Fragments with a Short-Read Sequencer and a Single-Tube Linked-Read Library Method

Targeted phasing of 2–200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method

Deciphering the tissue-specific functional effect of Alzheimer risk SNPs with deep genome annotation

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