Biology subjects

Neklason, D. W.

Publications and source records attributed to Neklason, D. W..

6 recordsLinked to original sources

bioRxiv2026

A family portrait of the genomic factors shaping tandem repeat mutagenesis

Tandem repeats (TRs) are among the most mutable loci in the human genome, but the genomic determinants of TR mutagenesis remain mysterious. We used PacBio HiFi long-read sequencing to profile nearly eight million TR loci in 28 members of a large, four-generation CEPH/Utah family designated K1463. We identified 1,270 de novo TR expansions and contractions across 20 children in the pedigree. De novo mutations (DNMs) were more likely to occur at loci that were longer, composed of uninterrupted motif sequences, and heterozygous in the parental germline. Children born to older fathers also exhibited more de novo mutations at short tandem repeats (STRs). A total of 43 TR loci were hyper-mutable in K1463, expanding or contracting up to twelve times across the pedigree. Among hyper-mutable loci that comprised multiple motifs (i.e., "complex" loci), specific motifs expanded and contracted more often than others; for example, all ten DNMs at a complex, hyper-mutable locus near the non-coding RNA LINC03021 involved the same 19bp motif. The mutability of particular motifs may be attributable to allele length, as 95% of DNMs at complex loci were expansions and contractions of the most abundant motif on a parental haplotype. However, future work will be required to disentangle the effects of nucleotide content and allele length on motif-specific mutability, especially at hyper-mutable TRs. Overall, this study combines long-read sequencing technologies with new software tools to comprehensively investigate the factors that influence TR mutagenesis.

genomics↗

bioRxiv2025

Human acrocentric chromosome short arm de novo mutation and recombination

The extraordinary repetitive content of human acrocentric short arms has prevented detailed investigations into recombination and de novo mutation. Integrating multiple sequencing technologies, we created 156 phased short arms and assessed 107 intergenerational transmissions from 23 samples in a four-generation pedigree. We observed a significant depletion (P<0.0001) of p-arm allelic recombination but one ectopic chr13-chr21 recombination breakpoint mediated by a 630 kbp segmental duplication mapping 1.6 Mbp distal to the SST1 array. In contrast, 18 maternal-biased q-arm allelic recombinations are significantly enriched within 5 Mbp of the centromere. Compared to autosomal euchromatin, the overall p-arm de novo single-nucleotide variant rate (1.33x10- per base pair per generation) is 10-fold higher, with a significant reduction of C>T but increased C>G and A>C mutations. We hypothesize that acrocentric sequence composition biases and the dearth of allelic recombination contribute to an elevated mutation rate and unique mutational signatures suggestive of mismatch repair defects and oxidative stress-induced DNA lesions.

genomics↗

bioRxiv2025

AVITI sequencing of a four-generation CEPH/Utah pedigree confirms low mutation rates at homopolymer loci despite their low sequence complexity

BackgroundShort tandem repeats (STRs) and homopolymers are among the most mutable loci in the human genome. Despite their presumed mutability owing to replication slippage, homopolymer loci exhibit lower mutation rates and minimal paternal age effects compared to other STRs. This paradox questions if technical limitations, rather than biological mechanisms, explain these observations. ResultsWe used the Element Biosciences AVITI platform to sequence the genomes of a 48-member, four-generation CEPH/Utah pedigree. As the AVITI platform reduces error rates at repetitive sequences compared to Illumina, this design enabled accurate mutation discovery at 90% of assayed homopolymers and a 1.7-fold increase in discoverable mutations compared to Illumina. We identified a median of 35 de novo homopolymer mutations per trio and a mutation rate of 5.28 x 10-5 DNMs per locus per generation, confirming a lower rate than dinucleotides (1.94 x 10-4). Most DNMs were single base-pair expansions or contractions. Despite comprising <1% of homopolymer loci, G/C homopolymers showed 18-fold higher mutation rates than A/T homopolymers; in contrast, the high dinucleotide mutation rate is not driven by a particular motif class. Parent-of-origin analysis revealed 78% of homopolymer mutations are paternal in origin, but no significant paternal age effect was observed. ConclusionsThis study confirms that homopolymers exhibit lower mutation rates and lack strong paternal age effects compared to other STRs, likely owing to the combination of a lower propensity to form slippage-causing secondary structures and more efficient mismatch repair. Our set of high-quality mutations suggest these phenomena are biological rather than technical in nature. Finally, we demonstrate that AVITI sequencing unlocks previously intractable regions of the genome and will be a powerful tool for continued investigation of repeat mutation.

genomics↗

bioRxiv2024

The Platinum Pedigree: A long-read benchmark for genetic variants

Recent advances in genome sequencing have improved variant calling in complex regions of the human genome. However, it is difficult to quantify variant calling performance since existing standards often focus on specificity, neglecting completeness in difficult to analyze regions. To create a more comprehensive truth set, we used Mendelian inheritance in a large pedigree (CEPH-1463) to filter variants across Illumina, PacBio high-fidelity (HiFi), and Oxford Nanopore Technologies platforms. This generated a variant map with over 4.7 million single-nucleotide variants, 767,795 indels, 537,486 tandem repeats, and 24,315 structural variants, covering 2.77 Gb of the GRCh38 genome. This work adds [~]200 Mb of high-confidence regions, including 8% more small variants, and introduces the first tandem repeat and structural variant truth sets for NA12878. As an example of the value of this improved benchmark, we retrained DeepVariant using this data to reduce genotyping errors by [~]34%.

genomics↗

bioRxiv2019

A novel ribosomal protein 20 variant in a family with unexplained colorectal cancer and polyposis

Colorectal cancer (CRC) has a large hereditary component, which is only partially explained by known genetic causes. Recently, variants in ribosomal protein S20 (RPS20, [OMIM: 603682]) were identified in a family with familial CRC type X and in a CRC cancer case-control screen. This study describes a novel splice donor variant in RPS20, NM_001023.3:c.177+1G>A. It segregates with CRC [OMIM: 114500] and polyposis [HP: 0200063] within the probands family. Reverse transcription-polymerase chain reaction (RT-PCR) confirms the variant results in two aberrantly-spliced transcripts that are absent in controls. The location of the novel RPS20 variant is near two previously-reported truncating RPS20 variants associated with CRC. DNA from colon adenocarcinoma showed no evidence of loss-of-heterozygosity, supporting a haploinsufficiency or dominant negative disease mechanism. These findings support designation of RPS20 as a CRC predisposition gene, and expand the phenotypic spectrum of RPS20 truncating variants to include polyposis.

genetics↗

bioRxiv2017

Universal Panel Testing of Pancreatic Cancer Cases for Cancer Predisposition

Background and AimsGenes associated with hereditary breast and ovarian cancer (HBOC) and colorectal cancer (CRC) susceptibility have been shown to play a role in pancreatic cancer susceptibility. Germline genetic testing of pancreatic cancer cases could be beneficial for at-risk relatives with pathogenic variants in established HBOC and CRC genes, but it is unclear what proportion of pancreatic cancer cases harbor pathogenic variants in these genes.\n\nMethods66 pancreatic cancer cases, unselected for family history and diagnosed at the Huntsman Cancer Hospital (HCH), were sequenced on a custom 34-gene panel including known HBOC and CRC genes. A second set of 156 unselected HCH pancreatic cancer cases were sequenced on an expanded 59-gene panel (n=95) or with a custom 14-gene clinical panel (n=61). Sequencing data from both sets of pancreatic cancer cases, the pancreatic cancer cases of the Cancer Genome Atlas (TCGA), and an unselected pancreatic cancer screen from the Mayo Clinic were combined in a meta-analysis to estimate the proportion of carriers with pathogenic and variants of uncertain significance.\n\nResultsApproximately 8.9% of unselected pancreatic cancer cases at the HCH carried a variant with potential HBOC or CRC screening recommendations. A meta-analysis of unselected pancreatic cancer cases revealed that approximately 10.5% carry a pathogenic variant or HiP-VUS.\n\nConclusionWith the inclusion of both HBOC and CRC susceptibility genes in a panel test, unselected pancreatic cancer cases have a high enough percentage of carriers to rationalize genetic testing for identification of variants that could be further used in cascade testing of healthy relatives to increase HBOC and CRC surveillance measures.

genetics↗