Dataset Information

JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts.

ABSTRACT:

Motivation

To increase detection power, researchers use gene level analysis methods to aggregate weak marker signals. Due to gene expression controlling biological processes, researchers proposed aggregating signals for expression Quantitative Trait Loci (eQTL). Most gene-level eQTL methods make statistical inferences based on (i) summary statistics from genome-wide association studies (GWAS) and (ii) linkage disequilibrium patterns from a relevant reference panel. While most such tools assume homogeneous cohorts, our Gene-level Joint Analysis of functional SNPs in Cosmopolitan Cohorts (JEPEGMIX) method accommodates cosmopolitan cohorts by using heterogeneous panels. However, JEPGMIX relies on brain eQTLs from older gene expression studies and does not adjust for background enrichment in GWAS signals.

Results

We propose JEPEGMIX2, an extension of JEPEGMIX. When compared to JPEGMIX, it uses (i) cis-eQTL SNPs from the latest expression studies and (ii) brains specific (sub)tissues and tissues other than brain. JEPEGMIX2 also (i) avoids accumulating averagely enriched polygenic information by adjusting for background enrichment and (ii) to avoid an increase in false positive rates for studies with numerous highly enriched (above the background) genes, it outputs gene q-values based on Holm adjustment of P-values.

Availability and implementation

https://github.com/Chatzinakos/JEPEGMIX2.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Chatzinakos C

PROVIDER: S-EPMC5860197 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts.

Chatzinakos Chris C Lee Donghyung D Webb Bradley T BT Vladimirov Vladimir I VI Kendler Kenneth S KS Bacanu Silviu-Alin SA

Bioinformatics (Oxford, England) 20180101 2

<h4>Motivation</h4>To increase detection power, researchers use gene level analysis methods to aggregate weak marker signals. Due to gene expression controlling biological processes, researchers proposed aggregating signals for expression Quantitative Trait Loci (eQTL). Most gene-level eQTL methods make statistical inferences based on (i) summary statistics from genome-wide association studies (GWAS) and (ii) linkage disequilibrium patterns from a relevant reference panel. While most such tools ...[more]

PMID: 28968763

Similar Datasets

Project description:BackgroundAccurate restoration of joint line height and posterior offset in primary Total Knee Arthroplasty (TKA) have been shown to be important factors in post-operative range of movement and function. The aim of this study was to assess the accuracy of joint line and posterior offset restoration in a group of patients that underwent robotic-assisted TKA (raTKA). A matched cohort of patients that underwent a TKA using a conventional jig-based technique was assessed for comparison. The null hypothesis was that there would be no difference between groups.MethodsThis study was a retrospective analysis of a cohort of 120 patients with end-stage knee osteoarthritis that received a TKA using the Navio Surgical System (n = 60), or Conventional manual TKA (n = 60). Procedures were performed between 1 January 2019 and 1 October 2019 at six different centres. Joint line height and posterior offset was measured pre-operatively and post-operatively on calibrated weight bearing plain radiographs of the knee. Two observers performed measurements using validated measuring tools. A BMI and age-matched cohort of patients that underwent TKA using a conventional technique in the same six centres were assessed for comparison. Mean values, standard deviations and confidence intervals are presented for change and absolute change in joint line height and posterior offset. Student's t-test was used to compare the changes between techniques.ResultsPatients that underwent robotic-assisted TKA had joint line height and posterior offset restored more accurately than patients undergoing TKA using a conventional technique. Average change from pre-operative measurement in joint line height using raTKA was -0.38mm [95% CI: -0.79 to 0.03] vs 0.91 [0.14 to 1.68] with the conventional technique. Average absolute change in joint line height using raTKA was 1.96mm [1.74 to 2.18] vs 4.00mm [3.68 to 4.32] with the conventional technique. Average change in posterior offset using raTKA was 0.08mm [-0.40 to 0.56] vs 1.64mm [2.47 to 0.81] with the conventional technique. Average absolute change in posterior offset with raTKA was 2.19mm [1.92 to 2.46] vs 4.24mm [3.79 to 4.69] with the conventional technique. There was a significant difference when comparing absolute change in joint line height and posterior offset between groups (p<0.01).ConclusionRobotic-assisted primary TKA restores the joint line height and posterior offset more accurately than conventional jig-based techniques.

Dataset Information

JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts.

Motivation

Results

Availability and implementation

Supplementary information

Publications

JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets