Qian Liu

Roswell Park Cancer Institute · Department of Biostatistics and Bioinformatics

Background The increasing volume and complexity of genomic data pose significant challenges for effective data management and reuse. Public genomic data often undergo similar preprocessing across projects, leading to redundant or inconsistent datasets and inefficient use of computing resources. This is especially pertinent for bioinformaticians eng...

The Common Workflow Language (CWL) is used to provide portable and reproducible data analysis workflows across different tools and computing environments. We have developed Rcwl, an R interface to CWL, to provide easier development, use, and maintenance of CWL pipelines from within R. We have also collected more than 100 pre-built tools and pipelin...

Graft-versus-host disease (GVHD) and infections are the 2 main causes of death without relapse after allogeneic hematopoietic cell transplantation (HCT). Elevated soluble serum simulation-2 (sST2), the product of IL1RL1 in plasma/serum post-HCT, is a validated GVHD biomarker. Hundreds of SNPs at 2q12.1 have been shown to be strongly associated with...

Despite the identification of several ovarian cancer (OC) predisposition genes, a large proportion of familial OC risk remains unexplained. We adopted a two‐stage design to identify new OC predisposition genes. We first carried out a large germline whole‐exome sequencing study on 158 patients from 140 families with significant OC history, but witho...

As next-generation sequencing (NGS) technology has become widely used to identify genetic causal variants for various diseases and traits, a number of packages for checking NGS data quality have sprung up in public domains. In addition to the quality of sequencing data, sample quality issues, such as gender mismatch, abnormal inbreeding coefficient...

Young black women are at higher risk of triple‐negative breast cancer (TNBC); however, a majority of the genetic studies on cancer predisposition were carried out in White populations. The underrepresentation of minority racial/ethnic populations in cancer genetic studies may have led to disproportionate gaps in our knowledge of cancer predispositi...

The last two authors contributed equally Elevated soluble Stimulation-2 (sST2), the decoy IL-33 receptor, in plasma/serum post-HSCT is a biomarker for death due to GvHD. ST2 is the product of IL1RL1 (2q12.1) and this ~.5Mb region contains >300 single nucleotide polymorphisms (SNPs) significantly associated (P<5x10-8) with plasma levels of sST2 in h...

Key Points We conducted the first exome-wide association study between germ line variant genotype and survival outcomes after unrelated-donor BMT. A number of novel genes were found to significantly affect survival outcomes.

The incidence and mortality rates of B-cell acute lymphoblastic leukemia (B-ALL) differ by age and sex. To determine if inherited genetic susceptibility contributes to these differences we performed 2 genome-wide association studies (GWAS) by age, sex, and subtype and subsequent meta-analyses. The GWAS included 446 B-ALL cases, and 3027 healthy unr...

Key Points Candidate SNP associations with survival outcomes after URD transplant are most likely false-positive findings. Over 85% of candidate SNPs are not linked to a biochemical function; of those that are, about half are not linked to the candidate gene.

Over the past decade, there have been numerous published candidate gene association studies of non-HLA variants, genes and/or pathways in relation to BMT survival outcomes. Most of these studies investigated a small number of candidate single nucleotide polymorphisms (SNPs), chosen based on known gene function, in a limited number of cases without...

#the authors contributed equally to this work While survival outcomes after HLA-matched unrelated donor (URD) blood and marrow transplant (BMT) have significantly improved over the last two decades, about 40% of patients die before 1-year post URD BMT. Previously we performed a genome-wide association study (GWAS) named DISCOVeRY-BMT (Determining t...

Both genome wide association studies (GWAS) of common variation and exome wide association studies (EXWAS) of rare variation have successfully identified disease susceptibility variants for a variety of diseases. One GWAS of inherited susceptibility to Acute Myeloid Leukemia (AML) has been conducted, but no EXWAS have been performed to measure risk...

Leveraging population-distinct linkage equilibrium (LD) patterns, trans-ethnic follow-up of variants discovered from genome-wide association studies (GWAS) has proved to be useful in facilitating the identification of bona fide causal variants. We previously developed the preferential LD approach, a novel method that successfully identified causal...

Breast cancer-related lymphedema (BCRL) is a serious chronic condition after breast cancer (BC) surgery and treatment. It is unclear if BCRL risk varies by race/ethnicity. In a multiethnic prospective cohort study of 2953 BC patients, we examined the association of self-reported BCRL status with self-reported race/ethnicity and estimated genetic an...

It is common and advantageous for researchers to combine RNA-seq data from similar studies to increase statistical power in genomics analysis. However the unwanted noise and hidden ar-tifacts such as batch effects could dramatically reduce the accuracy of statistical inference. The performance of three different methods, SVA, ComBat and PCA, for co...

While survival outcomes after HLA-matched unrelated donor (URD) blood and marrow transplant (BMT) have significantly improved over the last 2 decades, about 40% of patients die of various causes before one-year post-URD BMT. We performed a genome-wide association study (GWAS) named DISCOVeRY-BMT (Determining the Influence of Susceptibility COnveyin...

Transplant-related mortality (TRM) is the largest limiting factor to successful URD-BMT as curative therapy. Identification of non-HLA genetic factors in either recipients or donors could improve BMT outcomes through better matching at these loci. We performed a genome-wide association study (GWAS), named DISCOVeRY-BMT (Determining the Influence of...

Inherited genetic polymorphisms in ARID5B, GATA3, and IKZF1 have been reported to be associated with ALL and vary by cytogenetic subgroups. For example, ARID5B variants are associated with hyperdiploid B-ALL in pediatric patients, which occurs in approximately 30% of ALL patients and is a marker of good prognosis. In contrast, a variant in GATA3 (r...

Genotype imputation has been widely adopted in the postgenome-wide association studies (GWAS) era. Owing to its ability to accurately predict the genotypes of untyped variants, imputation greatly boosts variant density, allowing fine-mapping studies of GWAS loci and large-scale meta-analysis across different genotyping arrays. By leveraging genotyp...

Background: HER2 status is an integral part of breast cancer management. One of the variables that negatively affects HER2 test is delay to formalin fixation (DFF). The purpose of this study is to determine the effect of progressive DFF on HER2-dual color in situ hybridization (Dual-ISH). Materials and methods: Ten palpable invasive breast cance...