Arjun Biddanda
A5084980433- Genetic Associations and Epidemiology
- Genetic Mapping and Diversity in Plants and Animals
- Evolution and Genetic Dynamics
- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Forensic and Genetic Research
- Chromosomal and Genetic Variations
- Genomics and Rare Diseases
- Race, Genetics, and Society
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Mitochondrial Function and Pathology
- Yersinia bacterium, plague, ectoparasites research
- Genetic and phenotypic traits in livestock
- Advanced Proteomics Techniques and Applications
- Asthma and respiratory diseases
- Microbial Metabolic Engineering and Bioproduction
- Helicobacter pylori-related gastroenterology studies
- Epigenetics and DNA Methylation
- Cancer Genomics and Diagnostics
- Genetic Neurodegenerative Diseases
- Forensic Anthropology and Bioarchaeology Studies
- Primate Behavior and Ecology
- Genomics and Chromatin Dynamics
- Genetics and Neurodevelopmental Disorders
- Nutritional Studies and Diet
Johns Hopkins University
2023-2025
University of Chicago
2018-2024
Addgene
2023
University of Oxford
2021-2023
Zero to Three
2023
Duke University
2020
National Institute of General Medical Sciences
2020
Cornell University
2014-2016
Heilongjiang Institute of Technology
2015
Harbin Institute of Technology
2015
The Yamnaya expansions from the western steppe into Europe and Asia during Early Bronze Age (~3000 BCE) are believed to have brought with them Indo-European languages possibly horse husbandry. We analyzed 74 ancient whole-genome sequences across Inner Anatolia show that Botai people associated earliest husbandry derived a hunter-gatherer population deeply diverged Yamnaya. Our results also suggest distinct migrations bringing West Eurasian ancestry South before after, but not at time of,...
Abstract Genome-wide genealogies compactly represent the evolutionary history of a set genomes and inferring them from genetic data has potential to facilitate wide range analyses. We introduce method, ARG-Needle, for accurately biobank-scale sequencing or genotyping array data, as well strategies utilize perform association other complex trait use these methods build genome-wide using 337,464 UK Biobank individuals test across seven traits. Genealogy-based detects more rare ultra-rare...
Abstract Apes possess two sex chromosomes—the male-specific Y chromosome and the X chromosome, which is present in both males females. The crucial for male reproduction, with deletions being linked to infertility 1 . vital reproduction cognition 2 Variation mating patterns brain function among apes suggests corresponding differences their chromosomes. However, owing repetitive nature incomplete reference assemblies, ape chromosomes have been challenging study. Here, using methodology...
Genetic variation that influences gene expression and splicing is a key source of phenotypic diversity
Abstract The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies 1–3 . Consequently, our understanding the evolution species is incomplete. Here we present haplotype-resolved reference analyses six species: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan siamang. We achieve chromosome-level contiguity with substantial sequence accuracy (<1 error in 2.7 megabases) completely 215 gapless chromosomes...
XWAS is a new software suite for the analysis of X chromosome in association studies and similar genetic studies. The plays an important role human disease traits many species, especially those with sexually dimorphic characteristics. Special attention needs to be given its due unique inheritance pattern, which leads analytical complications that have resulted majority genome-wide (GWAS) either not considering or mishandling it toolsets had been designed non-sex chromosomes. We hence...
We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran siamang. achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. resolve challenging regions, such as the major histocompatibility complex immunoglobulin loci, providing more in-depth evolutionary insights. Comparative...
A key challenge in human genetics is to understand the geographic distribution of genetic variation. Often variation described by showing relationships among populations or individuals, drawing inferences over many variants. Here, we introduce an alternative representation that reveals relative abundance different allele frequency patterns. This approach allows viewers easily see several features structure: (1) most variants are rare and geographically localized, (2) common a single region...
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains major obstacle. Today, more realistic are possible thanks to large increases quantity quality available genetic data, sophistication inference simulation software. However, implementing these still requires substantial time specialized knowledge. These challenges especially pronounced simulating genomes...
Abstract Apes possess two sex chromosomes—the male-specific Y and the X shared by males females. The chromosome is crucial for male reproduction, with deletions linked to infertility. carries genes vital reproduction cognition. Variation in mating patterns brain function among great apes suggests corresponding differences their structure evolution. However, due highly repetitive nature incomplete reference assemblies, ape chromosomes have been challenging study. Here, using state-of-the-art...
Conventional genome mapping-based approaches systematically miss genetic variation, particularly in regions that substantially differ from the reference. To explore this hidden we examined unmapped and poorly mapped reads genomes of 640 human individuals South Asian (SAS) populations 1000 Genomes Project Simons Genome Diversity Project. We assembled tens megabases non-redundant sequence thousands large contigs, much which is present both SAS non-SAS populations. demonstrated not discovered...
The leading cause of human pregnancy loss is aneuploidy, often tracing to errors in chromosome segregation during female meiosis. While abnormal crossover recombination known confer risk for limited data have hindered understanding the potential shared genetic basis these key molecular phenotypes. To address this gap, we performed retrospective analysis preimplantation testing from 139,416 vitro fertilized embryos 22,850 sets biological parents. By transmission haplotypes, identified...
The Bene Israel Jewish community from West India is a unique population whose history before the 18th century remains largely unknown. members consider themselves as descendants of Jews, yet identity ancestors and their arrival time to are unknown, with speculations on varying between 8th BCE 6th CE. Here, we characterize genetic by collecting genotyping 18 individuals. Combining 486 individuals 41 other Jewish, Indian Pakistani populations, additional worldwide conducted comprehensive...
African populations have been drastically underrepresented in genomics research, and failure to capture the genetic diversity across numerous ethnolinguistic groups (ELGs) found on continent has hindered equity of precision medicine initiatives globally. Here, we describe whole-genome sequencing 449 Nigerian individuals 47 unique self-reported ELGs. Population structure analysis reveals differentiation among our ELGs, consistent with previous findings. From 36 million SNPs insertions or...
Cochin Jews form a small and unique community on the Malabar coast in southwest India. While arrival time of any putative Jewish ancestors has been speculated to have taken place as far back biblical times (King Solomon's era), documented only since 9th century CE. Here, we explore genetic history by collecting genotyping 21 members combining data with that 707 individuals from 72 other Indian, Jewish, Pakistani populations, together additional worldwide populations. We applied comprehensive...
Asthma is the most common chronic disease in children, occurring at higher frequencies and with more severe children African ancestry. We tested for association haplotypes replicated significant childhood-onset asthma locus 17q12-q21 European American children. Following this, we used whole-genome sequencing data from 1060 100 individuals to identify novel variants on a high-risk American-specific haplotype. characterized these silico using gene expression ATAC-seq airway epithelial cells,...
Abstract/Summary Genetic variation influencing gene expression and splicing is a key source of phenotypic diversity. Though invaluable, studies investigating these links in humans have been strongly biased toward participants European ancestries, diminishing generalizability hindering evolutionary research. To address limitations, we developed MAGE, an open-access RNA-seq data set lymphoblastoid cell lines from 731 individuals the 1000 Genomes Project spread across 5 continental groups 26...
Over the past decade, genomic data have contributed to several insights on global human population histories. These studies been met both with interest and critically, particularly by populations oral histories that are records of their often reference origins. While reported concordance between genetic histories, there is potential for tension may stem from being prioritized or used confirm community-based knowledge ethnography, especially if they differ. To investigate interplay we focused...
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains major obstacle. Today, more realistic are possible thanks to large increases quantity quality available genetic data, sophistication inference simulation software. However, implementing these still requires substantial time specialized knowledge. These challenges especially pronounced simulating genomes...
Abstract Archeogenetics has been revolutionary, revealing insights into demographic history and recent positive selection. However, most studies to date have ignored the nonrandom association of genetic variants at different loci (i.e. linkage disequilibrium). This may be in part because basic properties disequilibrium samples from times are still not well understood. Here, we derive several results for summary statistics haplotypic variation under a model with time-stratified sampling: (1)...
Abstract Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic data sets remains major obstacle. Today, more realistic are possible thanks to large increases quantity quality available genetic data, sophistication inference simulation software. However, implementing these still requires substantial time specialized knowledge. These challenges especially pronounced...
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic data sets remains major obstacle. Today, more realistic are possible thanks to large increases quantity quality available genetic data, sophistication inference simulation software. However, implementing these still requires substantial time specialized knowledge. These challenges especially pronounced simulating genomes...
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic data sets remains major obstacle. Today, more realistic are possible thanks to large increases quantity quality available genetic data, sophistication inference simulation software. However, implementing these still requires substantial time specialized knowledge. These challenges especially pronounced simulating genomes...
Abstract Accurate inference of gene genealogies from genetic data has the potential to facilitate a wide range analyses. We introduce method for accurately inferring biobank-scale genome-wide sequencing or genotyping array data, as well strategies utilize within linear mixed models perform association and other complex trait use these new methods build using 337,464 UK Biobank individuals detect associations in 7 traits. Genealogy-based detects more rare ultra-rare signals ( N = 133,...