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Your search keyword '"Alvarez Jerez, Pilar"' showing total 2 results
Start Over Author "Alvarez Jerez, Pilar" Publisher escholarship, university of california
2 results on '"Alvarez Jerez, Pilar"'

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

Author

Kolmogorov, Mikhail, Billingsley, Kimberley J, Mastoras, Mira, Meredith, Melissa, Monlong, Jean, Lorig-Roach, Ryan, Asri, Mobin, Alvarez Jerez, Pilar, Malik, Laksh, Dewan, Ramita, Reed, Xylena, Genner, Rylee M, Daida, Kensuke, Behera, Sairam, Shafin, Kishwar, Pesout, Trevor, Prabakaran, Jeshuwin, Carnevali, Paolo, Yang, Jianzhi, Rhie, Arang, Scholz, Sonja W, Traynor, Bryan J, Miga, Karen H, Jain, Miten, Timp, Winston, Phillippy, Adam M, Chaisson, Mark, Sedlazeck, Fritz J, Blauwendraat, Cornelis, and Paten, Benedict

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Neurosciences, Human Genome, Nanotechnology, Bioengineering, Neurodegenerative, Brain Disorders, Humans, Sequence Analysis, DNA, Haplotypes, Genome, Human, Nanopore Sequencing, Methylation, Pilot Projects, High-Throughput Nucleotide Sequencing, Technology, Medical and Health Sciences, Developmental Biology, Biological sciences
Abstract

Long-read sequencing technologies substantially overcome the limitations of short-reads but have not been considered as a feasible replacement for population-scale projects, being a combination of too expensive, not scalable enough or too error-prone. Here we develop an efficient and scalable wet lab and computational protocol, Napu, for Oxford Nanopore Technologies long-read sequencing that seeks to address those limitations. We applied our protocol to cell lines and brain tissue samples as part of a pilot project for the National Institutes of Health Center for Alzheimer's and Related Dementias. Using a single PromethION flow cell, we can detect single nucleotide polymorphisms with F1-score comparable to Illumina short-read sequencing. Small indel calling remains difficult within homopolymers and tandem repeats, but achieves good concordance to Illumina indel calls elsewhere. Further, we can discover structural variants with F1-score on par with state-of-the-art de novo assembly methods. Our protocol phases small and structural variants at megabase scales and produces highly accurate, haplotype-specific methylation calls.

Published
2023

2. Genome-wide structural variant analysis identifies risk loci for non-Alzheimer's dementias.

Author

Kaivola, Karri, Kaivola, Karri, Chia, Ruth, Ding, Jinhui, Rasheed, Memoona, Fujita, Masashi, Menon, Vilas, Walton, Ronald L, Collins, Ryan L, Billingsley, Kimberley, Brand, Harrison, Talkowski, Michael, Zhao, Xuefang, Dewan, Ramita, Stark, Ali, Ray, Anindita, Solaiman, Sultana, Alvarez Jerez, Pilar, Malik, Laksh, Dawson, Ted M, Rosenthal, Liana S, Albert, Marilyn S, Pletnikova, Olga, Troncoso, Juan C, Masellis, Mario, Keith, Julia, Black, Sandra E, Ferrucci, Luigi, Resnick, Susan M, Tanaka, Toshiko, American Genome Center, International LBD Genomics Consortium, International ALS/FTD Consortium, PROSPECT Consortium, Topol, Eric, Torkamani, Ali, Tienari, Pentti, Foroud, Tatiana M, Ghetti, Bernardino, Landers, John E, Ryten, Mina, Morris, Huw R, Hardy, John A, Mazzini, Letizia, D'Alfonso, Sandra, Moglia, Cristina, Calvo, Andrea, Serrano, Geidy E, Beach, Thomas G, Ferman, Tanis, Graff-Radford, Neill R, Boeve, Bradley F, Wszolek, Zbigniew K, Dickson, Dennis W, Chiò, Adriano, Bennett, David A, De Jager, Philip L, Ross, Owen A, Dalgard, Clifton L, Gibbs, J Raphael, Traynor, Bryan J, Scholz, Sonja W, Kaivola, Karri, Kaivola, Karri, Chia, Ruth, Ding, Jinhui, Rasheed, Memoona, Fujita, Masashi, Menon, Vilas, Walton, Ronald L, Collins, Ryan L, Billingsley, Kimberley, Brand, Harrison, Talkowski, Michael, Zhao, Xuefang, Dewan, Ramita, Stark, Ali, Ray, Anindita, Solaiman, Sultana, Alvarez Jerez, Pilar, Malik, Laksh, Dawson, Ted M, Rosenthal, Liana S, Albert, Marilyn S, Pletnikova, Olga, Troncoso, Juan C, Masellis, Mario, Keith, Julia, Black, Sandra E, Ferrucci, Luigi, Resnick, Susan M, Tanaka, Toshiko, American Genome Center, International LBD Genomics Consortium, International ALS/FTD Consortium, PROSPECT Consortium, Topol, Eric, Torkamani, Ali, Tienari, Pentti, Foroud, Tatiana M, Ghetti, Bernardino, Landers, John E, Ryten, Mina, Morris, Huw R, Hardy, John A, Mazzini, Letizia, D'Alfonso, Sandra, Moglia, Cristina, Calvo, Andrea, Serrano, Geidy E, Beach, Thomas G, Ferman, Tanis, Graff-Radford, Neill R, Boeve, Bradley F, Wszolek, Zbigniew K, Dickson, Dennis W, Chiò, Adriano, Bennett, David A, De Jager, Philip L, Ross, Owen A, Dalgard, Clifton L, Gibbs, J Raphael, Traynor, Bryan J, and Scholz, Sonja W

Abstract

We characterized the role of structural variants, a largely unexplored type of genetic variation, in two non-Alzheimer's dementias, namely Lewy body dementia (LBD) and frontotemporal dementia (FTD)/amyotrophic lateral sclerosis (ALS). To do this, we applied an advanced structural variant calling pipeline (GATK-SV) to short-read whole-genome sequence data from 5,213 European-ancestry cases and 4,132 controls. We discovered, replicated, and validated a deletion in TPCN1 as a novel risk locus for LBD and detected the known structural variants at the C9orf72 and MAPT loci as associated with FTD/ALS. We also identified rare pathogenic structural variants in both LBD and FTD/ALS. Finally, we assembled a catalog of structural variants that can be mined for new insights into the pathogenesis of these understudied forms of dementia.

Published
2023

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