Regulatory rare variants are associated with preterm birth

Genetic contributions to the risk of preterm birth have been extensively observed, yet the detailed nature of specific genetic component remains obscure. We analyzed the whole-genome sequencing data of several hundreds of families and found that the rare variant occurrence rate in gene regulatory regions is significantly correlated with gestational age in mothers. In contrast, the same correlations are insignificant for fathers, and coding regions show weaker correlations.

Key analyses:

  • QC of BAM files, variant calls and sample relatedness.
  • Variant calling pipeline.
  • Construction of a genetic variant database.
  • Population stratificaiton analysis.
  • Allele/genotype frequency computing.
  • Genome-wide association study.
  • Rare variant collapsing.
  • Genotype-phenotype associations.
  • Genomic control and nonparametric tests.
  • eQTL analysis.
  • Epistatic interaction analysis.

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

The MCScanX software package implements an advanced algorithm for detection of synteny and collinearity which also includes 14 utility programs for visualization of results and additional downstream analyses. The software was coded in C++, Perl and Java. Its paper was published in Nucleic Acids Research. MCScanX has become the standard approach for synteny and collinearity analysis and been cited over 180 times.

Genome sequencing projects citing MCScanX:

  • Structural and functional partitioning of bread wheat chromosome 3B. Science, 345(6194):1249721.
  • Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature, 500(7463):453-7.
  • The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature, 505(7484):546-9.
  • Genome sequence and genetic diversity of the common carp, Cyprinus carpio. Nat Genet, 46(11):1212-9.
  • Genome sequence of mungbean and insights into evolution within Vigna species. Nat Commun, 5:5443.
  • The tobacco genome sequence and its comparison with those of tomato and potato. Nat Commun, 5:3833.