The human and non-human primate developmental GTEx projects
dGTEx marker paper is now available online in Nature and has been featured by OHSU News. Congratulations to all! Abstract Many human diseases are the result of early developmental defects. As most paediatric diseases and disorders are rare, children are critically underrepresented in research. Functional genomics studies primarily rely on adult tissues and lack critical […]
Estimating realized relatedness in free-ranging macaques by inferring identity-by-descent segments
The latest NHP paper with contributions from the lab is now available online in PNAS. Congratulations! Significance Genetic relatedness plays a central role in ecology and evolution, but estimating it with high accuracy remains challenging. We established and validated a software pipeline that produces precise relatedness estimates for low-depth sequencing data by measuring the identical […]
Utility of exome sequencing in primary spermatogenic disorders: From research to diagnostics
Antoni and Liina’s review is now available online in Andrology. Congratulations! Abstract Background Primary spermatogenic disorders represent a severe form of male infertility whereby sperm production is impaired due to testicular dysfunction, leading to reduced quality or quantity of spermatozoa. Gene-centered research has certainly demonstrated the importance of the genetic factor in the etiology of […]
Introduction to androgenetics: terminology, approaches, and impactful studies across 60 years
Arvand’s review with Dr. Maris Laan from the University of Tartu in Estonia is now available online in Andrology. This is article is part of a Special Issue of Andrology “Genetics in Andrology. Congratulations! Abstract Across six decades, androgenetics has consistently concentrated on discovering genetic causes and enhancing the molecular diagnostics of male infertility, disorders […]
Diminished DNA binding affinity of DMRT1 caused by heterozygous DM domain mutations is a cause of male infertility
Helen’s paper with our Croatian collaborators in now available online in Human Molecular Genetics. Congratulations! Abstract The most severe form of male infertility is idiopathic non-obstructive azoospermia (NOA), a complete sperm absence in the ejaculate. We performed exome sequencing in the Croatian infertile brothers with NOA and found a variant in DMRT1 (Doublesex and mab-3 related transcription […]
PSAP-Genomic-Regions: A Method Leveraging Population Data to Prioritize Coding and Non-Coding Variants in Whole Genome Sequencing for Rare Disease Diagnosis
Marie-Sophie, who was a visiting scholar in the Conrad lab last summer, just had had paper published on extending PSAP to the non-coding genomes in Genetic Epidemiology. Congratulations! Abstract The introduction of Next-Generation Sequencing technologies in the clinics has improved rare disease diagnosis. Nonetheless, for very heterogeneous or very rare diseases, more than half of […]
The human infertility single-cell testis atlas (HISTA): an interactive molecular scRNA-Seq reference of the human testis
Eisa’s new paper is now available online in Andrology. Congratulations! Abstract Background: Single-cell RNA-seq (scRNA-Seq) has been widely adopted to study gene expression of the human testis. Several datasets of scRNA-Seq from human testis have been generated from different groups processed with different informatics pipelines. An integrated atlas of scRNA-Seq expression constructed from multiple donors, developmental […]
Genome sequencing of Pakistani families with male infertility identifies deleterious genotypes in SPAG6, CCDC9, TKTL1, TUBA3C, and M1AP
Muhammad’s paper on work he did during his six months as a visiting scholar in the Conrad lab is now available online In Andrology. Congratulations! Abstract Background: There are likely to be hundreds of monogenic forms of human male infertility. Whole genome sequencing (WGS) is the most efficient way to make progress in mapping the causative […]
A naturally occurring variant of MBD4 causes maternal germline hypermutation in primates
Alex’s paper is now available online in Genome Research. Congratulations! Abstract As part of an ongoing genome sequencing project at the Oregon National Primate Research Center, we identified a rhesus macaque with a rare homozygous frameshift mutation in the gene methyl-CpG binding domain 4, DNA glycosylase (MBD4). MBD4 is responsible for the repair of C […]
Consensus label propagation with graph convolutional networks for single-cell RNA sequencing cell type annotation
Daniel’s paper is now available online in Bioinformatics. Congratulations! Abstract Motivation: Single-cell RNA sequencing (scRNA-seq) data, annotated by cell type, is useful in a variety of downstream biological applications, such as profiling gene expression at the single-cell level. However, manually assigning these annotations with known marker genes is both time-consuming and subjective. Results: We present a Graph […]