涉及的領域主要是生物信息學、計算生物學和表觀遺傳學，同時會關注機器學習、統(tǒng)計、干細胞生物學、發(fā)育生物學、遺傳學、精準醫(yī)學等方向。
因為經(jīng)常去看新的發(fā)表的文章或者預印本，所以想著在這里寫個帖子，和大家分享下，并談談自己的想法和心得。
不一定全是剛出來的文章啦！
特別關注：單細胞、網(wǎng)絡生物學、算法、細胞命運決定、基因表達調(diào)控等。
2019年3月16日
1. An open resource of structural variation for medical and population genetics
https://www.biorxiv.org/content/10.1101/578674v1?Posted March 14, 2019.
原來的gnomAD數(shù)據(jù)庫是沒有Structure Variation相關資料的，這一次的更新是非常大的補充，很有價值，值得關注。
The gnomAD-SV resources have been integrated into the gnomAD browser (https://gnomad.broadinstitute.org), where users can freely explore this dataset without restrictions on reuse, which will have broad utility in population genetics, disease association, and diagnostic screening.
2. Fantom CAGE-seq 數(shù)據(jù)庫更新
http://fantom.gsc.riken.jp/5/datafiles/reprocessed/
hg38_latest/ 15-Mar-2019 18:28
mm10_latest/ 15-Mar-2019 18:31
2019年3月12日
1. Landscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes
https://www.biorxiv.org/content/10.1101/573378v2?(Posted March 10, 2019)
BioRxiv上更新了gnomAD的一個工作，gnomAD還是很有價值，蠻有意思的啦，好像還沒有正式發(fā)表的工作，該數(shù)據(jù)庫不僅包括外顯子測序數(shù)據(jù)，還包括全基因組測序數(shù)據(jù)。詳細介紹見于：https://gnomad.broadinstitute.org。今天訪問時，發(fā)現(xiàn)網(wǎng)站已經(jīng)改版了。
The data set provided on this website spans 125,748 exome sequences and 15,708 whole-genome sequences from unrelated individuals sequenced as part of various disease-specific and population genetic studies.
2. Interrogation of human hematopoiesis at single-cell and single-variant resolution
https://www.nature.com/articles/s41588-019-0362-6?Published: 11 March 2019
Nature Genetics上一篇分析UK Biobank的文章，有分析enhancer上的variant：
For regulatory variants, we explore patterns of developmental enhancer activity, predict molecular mechanisms, and identify likely target genes.
Our study provides a comprehensive framework for single-variant and single-cell analyses of genetic associations.
2019年3月10日
BioRxiv,?Posted March 09, 2019.
Whole exome sequencing and characterization of coding variation in 49,960 individuals in the UK Biobank
https://www.biorxiv.org/content/10.1101/572347v1
Abstract:
The UK Biobank is a prospective study of 502,543 individuals, combining extensive phenotypic and genotypic data with streamlined access for researchers around the world. Here we describe the first tranche of large-scale exome sequence data for 49,960 study participants, revealing approximately 4 million coding variants (of which ~98.4% have frequency < 1%). The data includes 231,631 predicted loss of function variants, a >10-fold increase compared to imputed sequence for the same participants. Nearly all genes (>97%) had ≥1 predicted loss of function carrier, and most genes (>69%) had ≥10 loss of function carriers. We illustrate the power of characterizing loss of function variation in this large population through association analyses across 1,741 phenotypes. In addition to replicating a range of established associations, we discover novel loss of function variants with large effects on disease traits, including PIEZO1 on varicose veins, COL6A1 on corneal resistance, MEPE on bone density, and IQGAP2 and GMPR on blood cell traits. We further demonstrate the value of exome sequencing by surveying the prevalence of pathogenic variants of clinical significance in this population, finding that 2% of the population has a medically actionable variant. Additionally, we leverage the phenotypic data to characterize the relationship between rare BRCA1 and BRCA2 pathogenic variants and cancer risk. Exomes from the first 49,960 participants are now made accessible to the scientific community and highlight the promise offered by genomic sequencing in large-scale population-based studies.
