We use cookies to understand how you use our site and to improve your experience. This includes personalizing content and advertising. To learn more, click here. By continuing to use our site, you accept our use of cookies. Cookie Policy.

Features Partner Sites Information LinkXpress hp
Sign In
Advertise with Us
LGC Clinical Diagnostics

Download Mobile App




Esophageal Cancer GWAS Leads to Risk Variants

By LabMedica International staff writers
Posted on 15 Feb 2018
Print article
Image: A histopathology of esophageal squamous cell carcinoma with keratin pearl formation (Photo courtesy of Dr. Dharam Ramnani, MD).
Image: A histopathology of esophageal squamous cell carcinoma with keratin pearl formation (Photo courtesy of Dr. Dharam Ramnani, MD).
Genome-wide association studies have identified common variants associated with risk of esophageal squamous cell carcinoma; however, these common variants cannot explain all heritability of esophageal cancer.

New germline contributors to esophageal squamous cell carcinoma (ESCC) risk have been revealed, including a low-frequency change to the Cytochrome P450 Family 26 Subfamily B Member 1, (CYP26B1) drug metabolism gene that appears to affect blood serum levels of a tumor suppressor called all-trans retinoic acid (atRA).

Scientists at the Chinese Academy of Medical Sciences (Beijing, China) and their colleagues used exome sequences for more than 3,700 individuals with ESCC and nearly 3,900 individuals without. They looked for single-nucleotide polymorphisms (SNPs) or low-frequency variants associated with risk of the disease, which is especially common in parts of China. From these data, they narrowed in on half a dozen risk sites that could be replicated in another 7,002 cases and 8,757 controls, including three common SNPs and three low-frequency variants.

The team used Illumina HumanExome BeadChip arrays to profile low-frequency protein-coding variants in the ESCC cases and the controls from Beijing. After excluding samples with insufficient or low-quality data, they were left comparing exome patterns for 3,714 of the ESCC cases and 3,880 controls, an analysis that led to 30 suspicious variants. The team attempted to verify the potential ESCC risk variants with OpenArray- or TaqMan-based genotyping on individuals from two replication cohorts: 3,120 ESCC cases and 3,919 controls from Wuhan province and another 3,882 individuals with ESCC and 4,838 without from the Chinese province of Hebei.

The scientists uncovered six new risk variants at four sites in or around the CCHCR1, TCN2, TNXB, LTA, CYP26B1, and FASN genes. Three of the associations at the TCN2, CYP26B1, and FASN gene loci, were based on low-frequency variants that appeared to have higher-than-usual effect sizes. An ESCC-associated variant at CYP26B1, called rs138478634, had particularly close ties to ESCC risk in individuals with a history of smoking and/or drinking, although the team noted that rs138478634 was not linked to smoking or drinking status in control individuals. Through a series of follow-up cell line and patient serum expression profiling experiments, the group saw lower-than-usual levels of the atRA tumor suppressor in cells or individuals pumping out the rs138478634 variant-containing version of CYP26B1.

The authors concluded that results of the new study extended previous findings and advanced our understanding of the genetic etiology of ESCC, which might be useful for risk assessment, early detection, and targeted treatment of ESCC. The study was published on January 29, 2018, in the journal Nature Genetics.

Related Links:
Chinese Academy of Medical Sciences

Gold Member
Chagas Disease Test
CHAGAS Cassette
Verification Panels for Assay Development & QC
Seroconversion Panels
New
Respiratory QC Panel
Assayed Respiratory Control Panel
New
Anti-HHV-6 IgM Assay
anti-HHV-6 IgM ELISA (semiquant.)

Print article

Channels

Clinical Chemistry

view channel
Image: The tiny clay-based materials can be customized for a range of medical applications (Photo courtesy of Angira Roy and Sam O’Keefe)

‘Brilliantly Luminous’ Nanoscale Chemical Tool to Improve Disease Detection

Thousands of commercially available glowing molecules known as fluorophores are commonly used in medical imaging, disease detection, biomarker tagging, and chemical analysis. They are also integral in... Read more

Immunology

view channel
Image: The cancer stem cell test can accurately choose more effective treatments (Photo courtesy of University of Cincinnati)

Stem Cell Test Predicts Treatment Outcome for Patients with Platinum-Resistant Ovarian Cancer

Epithelial ovarian cancer frequently responds to chemotherapy initially, but eventually, the tumor develops resistance to the therapy, leading to regrowth. This resistance is partially due to the activation... Read more

Microbiology

view channel
Image: The lab-in-tube assay could improve TB diagnoses in rural or resource-limited areas (Photo courtesy of Kenny Lass/Tulane University)

Handheld Device Delivers Low-Cost TB Results in Less Than One Hour

Tuberculosis (TB) remains the deadliest infectious disease globally, affecting an estimated 10 million people annually. In 2021, about 4.2 million TB cases went undiagnosed or unreported, mainly due to... Read more

Pathology

view channel
Image: The ready-to-use DUB enzyme assay kits accelerate routine DUB activity assays without compromising data quality (Photo courtesy of Adobe Stock)

Sensitive and Specific DUB Enzyme Assay Kits Require Minimal Setup Without Substrate Preparation

Ubiquitination and deubiquitination are two important physiological processes in the ubiquitin-proteasome system, responsible for protein degradation in cells. Deubiquitinating (DUB) enzymes contain around... Read more

Technology

view channel
Image: The HIV-1 self-testing chip will be capable of selectively detecting HIV in whole blood samples (Photo courtesy of Shutterstock)

Disposable Microchip Technology Could Selectively Detect HIV in Whole Blood Samples

As of the end of 2023, approximately 40 million people globally were living with HIV, and around 630,000 individuals died from AIDS-related illnesses that same year. Despite a substantial decline in deaths... Read more

Industry

view channel
Image: The collaboration aims to leverage Oxford Nanopore\'s sequencing platform and Cepheid\'s GeneXpert system to advance the field of sequencing for infectious diseases (Photo courtesy of Cepheid)

Cepheid and Oxford Nanopore Technologies Partner on Advancing Automated Sequencing-Based Solutions

Cepheid (Sunnyvale, CA, USA), a leading molecular diagnostics company, and Oxford Nanopore Technologies (Oxford, UK), the company behind a new generation of sequencing-based molecular analysis technologies,... Read more
Copyright © 2000-2025 Globetech Media. All rights reserved.