Article
Genetics & Heredity
Robin J. Hofmeister, Diogo M. Ribeiro, Simone Rubinacci, Olivier Delaneau
Summary: SHAPEIT5, a new phasing method, accurately processes large sequencing datasets and improves imputation accuracy by generating reference panels of haplotypes. The method was applied to UK Biobank data, which resulted in the identification of 549 genes with compound heterozygous loss-of-function events. The use of UK Biobank as a reference panel, coupled with SHAPEIT5 phasing, further enhances genotype imputation accuracy.
Article
Genetics & Heredity
Simone Rubinacci, Diogo M. Ribeiro, Robin J. Hofmeister, Olivier Delaneau
Summary: GLIMPSE is a new method for haplotype phasing and genotype imputation of low-coverage sequencing datasets, showing remarkable performance across different coverages and human populations. This method achieves genome imputation at a cost lower than US$1, outperforming other methods and improving imputation accuracy over the full allele frequency range. The study indicates the promising potential of low-coverage imputation and suggests a paradigm shift in the design of future genomic studies.
Article
Multidisciplinary Sciences
Adriano De Marino, Abdallah Amr Mahmoud, Madhuchanda Bose, Karatug Ozan Bircan, Andrew Terpolovsky, Varuna Bamunusinghe, Sandra Bohn, Umar Khan, Biljana Novkovic, Puya G. Yazdi
Summary: This study compared the latest versions of popular HMM-based tools for phasing and imputation, evaluated them using multiple metrics, and determined the best combinations for different situations and analysis needs. An automated pipeline was also created to optimize imputation results.
Review
Plant Sciences
Muhammad Yasir, Hafiza Hamrah Kanwal, Quaid Hussain, Muhammad Waheed Riaz, Muhammad Sajjad, Junkang Rong, Yurong Jiang
Summary: Over the past two decades, high-density SNP arrays and DNA sequencing technology have been widely used in crop research, particularly in cotton crops. Genome-wide association studies (GWAS) have provided an important tool for uncovering the relationship between crop phenotypes and underlying genetics, helping to advance crop breeding and improvement.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Jie Li, Jie Wu, Yunhua Jian, Zhanwei Zhuang, Yibin Qiu, Ruqu Huang, Pengyun Lu, Xiang Guan, Xiaoling Huang, Shaoyun Li, Li Min, Yong Ye
Summary: This study identified CCND2 and SHANK2 genes as important candidates affecting the backfat thickness (BF) trait in pigs. The results provide a deeper understanding of the genetic basis of pig carcass traits and have important implications for breeding pigs with superior carcass characteristics.
Article
Agriculture, Dairy & Animal Science
Gerardo A. Fernandes Junior, Roberto Carvalheiro, Henrique N. de Oliveira, Mehdi Sargolzaei, Roy Costilla, Ricardo V. Ventura, Larissa F. S. Fonseca, Haroldo H. R. Neves, Ben J. Hayes, Lucia G. de Albuquerque
Summary: The study investigated the feasibility of imputing whole-genome sequence in Nellore beef cattle, achieving high imputation accuracies per individual. The software-dependent SNP-wise imputation accuracy is particularly important for rare variants. The accuracy of imputation appears to be relatively independent of annotation classification.
GENETICS SELECTION EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Jeremiah H. Li, Chase A. Mazur, Tomaz Berisa, Joseph K. Pickrell
Summary: The study found that low-pass sequencing combined with genotype imputation not only significantly increases the statistical power for genome-wide association studies but also provides increased accuracy for polygenic risk prediction compared to genotyping arrays.
Article
Genetics & Heredity
Burak Yelmen, Aurelien Decelle, Linda Ongaro, Davide Marnetto, Corentin Tallec, Francesco Montinaro, Cyril Furtlehner, Luca Pagani, Flora Jay
Summary: Generative models have the potential to create high-quality synthetic genomic data, improving the imputation quality for low-frequency alleles while protecting individual privacy. This could provide valuable assets in genetic studies by offering an easy-access and anonymous alternative for private genetic databases.
Article
Biology
Guorong Yan, Xianxian Liu, Shijun Xiao, Wenshui Xin, Wenwu Xu, Yiping Li, Tao Huang, Jiangtao Qin, Lei Xie, Junwu Ma, Zhiyan Zhang, Lusheng Huang
Summary: Sequencing-based GWAS have proven useful in identifying causal associations between genetic variants and traits. In this study, genotype imputation was used to increase SNP density in a large-scale swine F-2 population, revealing key nucleotides influencing traits and proposing two candidate genes related to meat traits. The study also illustrated various scenarios researchers may encounter in imputation-based GWAS.
SCIENCE CHINA-LIFE SCIENCES
(2022)
Article
Agriculture, Multidisciplinary
Yan Sun, Yu-Hua Li, Chang-Heng Zhao, Jun Teng, Yong-Hui Wang, Tian-Qi Wang, Xiao-Yuan Shi, Zi-Wen Liu, Hai-Jing Li, Ji-Jing Wang, Wen-Wen Wang, Chao Ning, Chang-Fa Wang, Qin Zhang
Summary: This study identified candidate genes affecting the number of thoracic and lumbar vertebrae in Dezhou donkeys. These genes may be involved in embryonic development and bone formation, and could be good candidates for vertebral number traits.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2023)
Article
Plant Sciences
Catja Selga, Alexander Koc, Aakash Chawade, Rodomiro Ortiz
Summary: The study introduces a pipeline to reduce genotyping costs by decreasing the number of SNPs and individuals, as well as pruning for linkage disequilibrium. Both GWAS and GS analyses can be performed without loss of information, making them applicable to large potato breeding populations.
Article
Genetics & Heredity
Chun-Yu Wei, Jenn-Hwai Yang, Erh-Chan Yeh, Ming-Fang Tsai, Hsiao-Jung Kao, Chen-Zen Lo, Lung-Pao Chang, Wan-Jia Lin, Feng-Jen Hsieh, Saurabh Belsare, Anand Bhaskar, Ming-Wei Su, Te-Chang Lee, Yi-Ling Lin, Fu-Tong Liu, Chen-Yang Shen, Ling-Hui Li, Chien-Hsiun Chen, Jeffrey D. Wall, Jer-Yuarn Wu, Pui-Yan Kwok
Summary: The Taiwan Biobank has collected genetic information from both high-coverage whole-genome sequencing and genome-wide SNP data of individuals with Han Chinese ancestry, revealing the full range of genetic variation in this population. The study found that some individuals carry mutations related to autosomal recessive diseases, cancer-predisposing genes, and variants affecting drug response, highlighting the potential for genetic testing to improve clinical care.
NPJ GENOMIC MEDICINE
(2021)
Article
Biochemical Research Methods
Albert Rosenberger, Viola Tozzi, Heike Bickeboeller
Summary: This paper introduces an independent pair of accuracy measures, Iam hiQ, which can be applied to evaluate the output of all imputation software; by applying both measures to a large sample of the International Lung Cancer Consortium (ILCCO), meaningful thresholds for classifying markers of poor accuracy were found.
BMC BIOINFORMATICS
(2022)
Article
Plant Sciences
Behailu Mulugeta, Kassahun Tesfaye, Rodomiro Ortiz, Eva Johansson, Teklehaimanot Hailesilassie, Cecilia Hammenhag, Faris Hailu, Mulatu Geleta
Summary: The growing global demand for wheat for food is rising due to population growth and climate change. A genome-wide association study (GWAS) using 10,045 SNP markers was conducted to identify genomic regions associated with grain yield and related traits in Ethiopian durum wheat. The study revealed high heritability estimates and identified novel marker-trait associations (MTAs) that could potentially improve durum wheat production globally. The research also highlighted the importance of the Ethiopian durum wheat gene pool in this improvement.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Genetics & Heredity
Yichen Si, Brett Vanderwerff, Sebastian Zollner
Summary: Genotype imputation is crucial in human genetic studies, but current algorithms may have model misspecifications that limit the accurate imputation of rare variants. The probability of falsely imputed minor alleles decreases with reference sample size, but the proportion of erroneously imputed minor alleles depends on the allele count in the reference sample.
Article
Multidisciplinary Sciences
Shengkai Li, Bahnisikha Dutta, Sarah Cannon, Joshua J. Daymude, Ram Avinery, Enes Aydin, Andrea W. Richa, Daniel Goldman, Dana Randall
Summary: This study introduces a method for controlling robotic swarms at macro and micro scales through theoretical abstraction and experimental systems, exploring collective behaviors guided by physical interactions. The research shows that increasing interparticle attraction can lead to a transition from dispersed to compact phase, enabling the collective to perform emergent tasks.
Article
Computer Science, Theory & Methods
Tom Gur, Yang P. Liu, Ron D. Rothblum
Summary: Interactive proofs of proximity allow a sublinear-time verifier to check a given input close to the language with a small amount of communication with a powerful prover. This work considers two minimally interactive variants of such proofs systems, MA-proofs and AMPs, showing an exponential separation in their power. The notion of oblivious proofs of proximity is also discussed, revealing a quadratic difference between AMPs and MAPs.
COMPUTATIONAL COMPLEXITY
(2021)
Article
Computer Science, Theory & Methods
Oded Goldreich, Tom Gur
Summary: Universal Locally Verifiable Codes (Universal-LVCs) are codes that allow local testing of properties of the encoded inputs using short proofs. These codes are useful for encoding inputs under which a large family of properties can be locally testable using a short proof.
THEORETICAL COMPUTER SCIENCE
(2021)
Editorial Material
Genetics & Heredity
Kangcheng Hou, Arjun Bhattacharya, Rachel Mester, Kathryn S. Burch, Bogdan Pasaniuc
Article
Genetics & Heredity
Yi Ding, Kangcheng Hou, Kathryn S. Burch, Sandra Lapinska, Florian Prive, Bjarni Vilhjalmsson, Sriram Sankararaman, Bogdan Pasaniuc
Summary: The study shows that Bayesian PRS methods can estimate the individual PRS variance and generate well-calibrated credible intervals through posterior sampling. Analysis of real traits in the UK Biobank demonstrates that large uncertainty in polygenic risk score (PRS) estimates at the individual level impacts the interpretation of subsequent analyses such as PRS-based stratification.
Article
Biochemical Research Methods
Ruth Johnson, Kathryn S. Burch, Kangcheng Hou, Mario Paciuc, Bogdan Pasaniuc, Sriram Sankararaman
Summary: The study introduces a statistical framework to estimate regional polygenicity of complex traits, finding that anthropometric and blood pressure traits are highly polygenic with wide variation in regional polygenicity.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Genetics & Heredity
Kathryn S. Burch, Kangcheng Hou, Yi Ding, Yifei Wang, Steven Gazal, Huwenbo Shi, Bogdan Pasaniuc
Summary: Recent research shows that SNP heritability may not be the most relevant quantity for localizing high-effect/critical disease genes. By estimating gene-level heritability, we found that approximately 2.5% of genes have a rare-variant component, and only about 0.8% of genes have heritability exclusively from rare variants. These additional genes include 114 gene-trait pairs that were not detected by existing methods. The rare-variant component of gene-level heritability exhibits different trends compared to common-variant gene-level heritability.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Computer Science, Hardware & Architecture
Alessandro Chiesa, Michael A. Forbes, Tom Gur, Nicholas Spooner
Summary: This paper studies whether spatial isolation still suffices to unconditionally achieve zero knowledge even in the presence of quantum entanglement. The research shows that for every language in NEXP, there exists a 2-prover zero knowledge interactive proof that is sound against entangled provers.
JOURNAL OF THE ACM
(2022)
Article
Computer Science, Theory & Methods
Alessandro Chiesa, Tom Gur, Igor Shinkar
Summary: Locally correctable codes (LCCs) are error correcting codes that can correct any symbol of a corrupted codeword locally. Constructing LCCs with minimal block length and O(1)-query algorithms has been a central problem in algorithmic coding theory, and recent progress has been made in constructing relaxed LCCs.
SIAM JOURNAL ON COMPUTING
(2022)
Article
Multidisciplinary Sciences
Yi Ding, Kangcheng Hou, Ziqi Xu, Aditya Pimplaskar, Ella Petter, Kristin Boulier, Florian Prive, Bjarni J. Vilhjalmsson, Loes M. Olde Loohuis, Bogdan Pasaniuc
Summary: Polygenic scores (PGSs) have limited portability across different groupings of individuals, hindering their equitable use. We demonstrated that PGS accuracy decreases individual-to-individual along the continuum of genetic ancestries, even within traditionally labelled 'homogeneous' genetic ancestries. Our results highlight the need to move away from discrete genetic ancestry clusters towards the continuum of genetic ancestries when considering PGSs.
Proceedings Paper
Computer Science, Theory & Methods
Tom Gur, Noam Lifshitz, Siqi Liu
Summary: We prove hypercontractive inequalities on high dimensional expanders and use these inequalities to obtain certain properties.
PROCEEDINGS OF THE 54TH ANNUAL ACM SIGACT SYMPOSIUM ON THEORY OF COMPUTING (STOC '22)
(2022)
Proceedings Paper
Computer Science, Theory & Methods
Vahid R. Asadi, Alexander Golovnev, Tom Gur, Igor Shinkar
Summary: This research presents a new framework for designing worst-case to average-case reductions. By applying this framework, algorithms that are only correct on a small fraction of inputs can be transformed into algorithms that are correct on all inputs. This framework has been successfully applied to various computational models and solved fundamental problems.
PROCEEDINGS OF THE 54TH ANNUAL ACM SIGACT SYMPOSIUM ON THEORY OF COMPUTING (STOC '22)
(2022)
Proceedings Paper
Computer Science, Theory & Methods
Srinivasan Arunachalam, Alex B. Grilo, Tom Gur, Igor C. Oliveira, Aarthi Sundaram
Summary: This paper establishes the connection between the design of quantum algorithms and circuit lower bounds. It shows that even a marginal quantum speedup over generic learning algorithms would have significant consequences in complexity lower bounds.
2021 IEEE 62ND ANNUAL SYMPOSIUM ON FOUNDATIONS OF COMPUTER SCIENCE (FOCS 2021)
(2022)
Article
Computer Science, Theory & Methods
Tom Gur, Oded Lachish
Summary: Locally decodable codes have various applications, with recent constructions achieving a blocklength n = O(k(1+gamma)) for O(1)-query relaxed LDCs. However, a lower bound shows that achieving blocklength n = k(1+o(1)) for O(1)-query relaxed LDCs is not possible, resolving an open problem raised in 2004.
SIAM JOURNAL ON COMPUTING
(2021)
Proceedings Paper
Computer Science, Theory & Methods
Alessandro Chiesa, Tom Gur, Igor Shinkar
PROCEEDINGS OF THE THIRTY-FIRST ANNUAL ACM-SIAM SYMPOSIUM ON DISCRETE ALGORITHMS (SODA'20)
(2020)