Mingze He

People
Graduate Research Assistant, Lawrence-Dill Lab
Mingze He

PAST RESEARCH EXPERIENCES:

Whole genome exome capture project - Charactering Rare Coding Variation in Chinese Han Population Through Whole Genome Exome Sequencing. Through the investigation of the dataset of 1500 (700 control, 800 cases from a psoriasis project) Chinese Han (CH) people 30X whole genome exon capture, we would like to reveal the demographic and evolutionary forces that shape rare coding variation within and among populations. Thus we intend to:

a. Characterize features of rare coding variations in Chinese Han Population (CHP).
b. Detect the strength of purifyig selection on rare coding SNPs in CHP.
c. Explore the correlation between demographic explosive and excessof rare SNPs.
d. Infer Han population genetic architecture through comparison of both rare and common SNPs with CEU.
e. Produce valuable implication for further Chinese Han individual genome research from the insight of rare coding variants.

His work: Building up the analysis pipeline, involving QC for sequenced samples and raw reads, SNP calling at population level, phasing with and without reference panel, variants filtering and annotation, conducted PCA and Tajima D power evaluation at various sample scale. Demographic inference and selection simulation base on SFS.

Primate Whole-Exome capture based on human capture array - He evaluated the efficiency of using a human exome capture design for the selective enrichment of exonic regions of non-human primates We compared the exon sequence recovery in 9 chimpanzees, 2 crab-eating macaques and 8 Japanese macaques. Our findings indicate that use of a human design exon-capture array can provide efficient enrichment of non-human primate gene regions. Accordingly, use of the human exon-capture methods provides an attractive, cost-effective approach for the comparative analysis of non-human primate genomes, including gene-based DNA variant discovery.

PUBLICATIONS:

Jin X, He M, Ferguson B, Meng Y, Ouyang L, et al. (2012). An effort to Use Human-Based Exome Capture Methods to Analyze Chimpanzee and Macaque Exomes. PLoS ONE 7(7): e40637. doi: 10.1371/journal.pone.0040637
http://www.plosone.org/article/info%Adoi%2F10.1371%2Fjournal.pone.0040637#

Poster on ASHG (American Society of Human Genetics): Characterizing the adaptation to high altitude in Tibetans. E. Huerta-Sanchez(1), X. Jin(2), B. Peter(1), Y. Liang(2), M. He(2), et al. 1) Statistics and Integrative Biology, UC Berkeley, Berkeley, CA; 2) BGI, Beijing genomics institute, BGI-Shenzhen, China.

Area of Expertise: 
Bioinformatics
Contact
+1 515 294 5122
0035 Carver Co-Lab
Ames
IA
50011-3650