Rylee M. Genner

Haplotype-resolved DNA methylation at the APOE locus identifies allele-specific epigenetic signatures relevant to Alzheimer’s disease risk

Rylee M. Genner, Melissa Meredith, Kensuke Daida, Abraham Moller et autres

Abstract The APOE gene encodes a lipid transport protein central to Alzheimer’s disease (AD) pathogenesis. Three common alleles—ε2 (rs7412(C > T)), ε3 (reference), and ε4 (rs429358(T > C))—arise from two coding variants in exon 4 and confer distinct AD risk profiles, with …

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The complete genome of the KOLF2.1J reference iPSC line

Pilar Álvarez Jerez, Arang Rhie, Juhyun Kim, Prajna Hebbar et autres

While induced pluripotent stem cells (iPSCs) have gained popularity in studying neurodegenerative diseases, the heterogeneity of stem cells used across studies impacts cross-study comparison. The iPSC Neurodegenerative Disease Initiative (iNDI) selected the KOLF2.1J cell line and prioritized its use as a reference …

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Haplotype-Resolved DNA Methylation at the APOE Locus identifies Allele-Specific Epigenetic Signatures Relevant to Alzheimer’s Disease Risk

Rylee M. Genner, Melissa Meredith, Abraham Moller, Cory A. Weller et autres

Abstract The APOE gene encodes a key lipid transport protein and plays a central role in Alzheimer’s disease (AD) pathogenesis. Three common APOE alleles, ε2 (rs7412(C>T), ε3 (reference), and ε4 (rs429358(T>C)), arise from two coding variants in exon 4 and confer distinct …

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Assessing DNA methylation detection for primary human tissue using Nanopore sequencing

Rylee M. Genner, Stuart Akeson, Melissa Meredith, Pilar Álvarez Jerez et autres

DNA methylation most commonly occurs as 5-methylcytosine (5mC) in the human genome and has been associated with human diseases. Recent developments in single-molecule sequencing technologies (Oxford Nanopore Technologies [ONT] and Pacific Biosciences [PacBio]) have enabled readouts of long, native DNA molecules, including …

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The Utility of Long‐Read Sequencing in Diagnosing Early Onset Parkinson's Disease

Kensuke Daida, Hiroyo Yoshino, Laksh Malik, Breeana Baker et autres

OBJECTIVE: Variants in PRKN and PINK1 are the leading cause of early-onset autosomal recessive Parkinson's disease, yet many cases remain genetically unresolved. We previously identified a 7 megabases complex structural variant in a pair of monozygotic twins using Oxford Nanopore Technologies (ONT) …

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Haplotype-Resolved Long-Read Sequencing in Hundreds of Diverse Brains Identifies Structural Variant Impacts on Expression and Allele-Specific Methylation

Melissa Meredith, Kensuke Daida, Abraham Moller, Pilar Álvarez Jerez et autres

Structural variants (SVs) drive gene expression in the human brain and are causative of many neurological conditions. However, most existing genetic studies have been based on short-read sequencing methods, which capture fewer than half of the SVs present in any one individual. …

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The Utility of Long-Read Sequencing in Diagnosing Genetic Autosomal Recessive Parkinson’s Disease: a genetic screening study

Kensuke Daida, Hiroyo Yoshino, Laksh Malik, Breeana Baker et autres

Abstract Background Mutations within the genes PRKN and PINK1 are the leading cause of early onset autosomal recessive Parkinson’s disease (PD). However, the genetic cause of most early-onset PD (EOPD) cases still remains unresolved. Long-read sequencing has successfully identified many pathogenic structural …

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Assessing methylation detection for primary human tissue using Nanopore sequencing

Rylee M. Genner, Stuart Akeson, Melissa Meredith, Pilar Álvarez Jerez et autres

DNA methylation most commonly occurs as 5-methylcytosine (5-mC) in the human genome and has been associated with human diseases. Recent developments in single-molecule sequencing technologies (Oxford Nanopore Technologies (ONT) and Pacific Biosciences) have enabled readouts of long, native DNA molecules, including cytosine …

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Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation

Mikhail Kolmogorov, Kimberley J. Billingsley, Mira Mastoras, Melissa Meredith et autres

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Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation

Mikhail Kolmogorov, Kimberley J. Billingsley, Mira Mastoras, Melissa Meredith et autres

Long-read sequencing technologies substantially overcome the limitations of short-reads but to date have not been considered as feasible replacement at scale due to a combination of being too expensive, not scalable enough, or too error-prone. Here, we develop an efficient and scalable …

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