Next Generation DNA-based Diagnostics and Discovery

Is renal cell carcinoma associated with MITF c.952G>A (p.E318K)?

P Harraka, F Bruinsma, T Nguyen-Dumont, S Jordan, GG Giles, IM Winship, K Tucker, MC Southey

2024-09-24

Prevalence of Germline Pathogenic Variants in Renal Cancer Predisposition Genes in a Population-Based Study of Renal Cell Carcinoma

F Bruinsma, P Harraka, S Jordan, DJ Park, B Pope, J Steen, RL Milne, GG Giles, I Winship, KM Tucker, MC Southey, T Nguyen-Dumont

2024-09-01

Renal cell carcinoma (RCC) has been associated with germline pathogenic or likely pathogenic (PLP) variants in recognised cancer s..

Hi-plex for simple, accurate, and cost-effective amplicon-based targeted DNA sequencing

BJ Pope, F Hammet, T Nguyen-Dumont, DJ Park

2018-01-01

Hi-Plex is a suite of methods to enable simple, accurate, and cost-effective highly multiplex PCR-based targeted sequencing (Nguye..

Mutation screening of ACKR3 and COPS8 in kidney cancer cases from the CONFIRM study

M Mahmoodi, T Nguyen-Dumont, F Hammet, BJ Pope, DJ Park, MC Southey, JM Darlow, F Bruinsma, I Winship

2017-07-01

An apparently balanced t(2;3)(q37.3;q13.2) translocation that appears to segregate with renal cell carcinoma (RCC) has indicated p..

UNDR ROVER - a fast and accurate variant caller for targeted DNA sequencing

DJ Park, R Li, E Lau, P Georgeson, T Nguyen-Dumont, BJ Pope

2016-04-16

Background: Previously, we described ROVER, a DNA variant caller which identifies genetic variants from PCR-targeted massively par..

AmpliVar: Mutation detection in high-throughput sequence from amplicon-based libraries

AL Hsu, O Kondrashova, S Lunke, CJ Love, C Meldrum, R Marquis-Nicholson, G Corboy, K Pham, M Wakefield, PM Waring, GR Taylor

2015-04-01

Conventional means of identifying variants in high-throughput sequencing align each read against a reference sequence, and then ca..

Hi-Plex targeted sequencing is effective using DNA derived from archival dried blood spots

T Nguyen-Dumont, M Mahmoodi, F Hammet, T Tran, H Tsimiklis, GG Giles, JL Hopper, MC Southey, DJ Park

2015-02-01

Many genetic epidemiology resources have collected dried blood spots (predominantly as Guthrie Cards) as an economical and efficie..

Abridged adapter primers increase the target scope of Hi-Plex

T Nguyen-Dumont, F Hammet, M Mahmoodi, BJ Pope, GG Giles, JL Hopper, MC Southey, DJ Park

2015-01-01

Previously, we reported Hi-Plex, an amplicon-based method for targeted massively parallel sequencing capable of generating 60 ampl..

ROVER variant caller: Read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets

BJ Pope, T Nguyen-Dumont, F Hammet, DJ Park

2014-01-24

Background: We recently described Hi-Plex, a highly multiplexed PCR-based target-enrichment system for massively parallel sequenci..

Hi-Plex for high-throughput mutation screening: Application to the breast cancer susceptibility gene PALB2

T Nguyen-Dumont, ZL Teo, BJ Pope, F Hammet, M Mahmoodi, H Tsimiklis, N Sabbaghian, M Tischkowitz, WD Foulkes, GG Giles, JL Hopper, MC Southey, DJ Park

2013-11-18

Background: Massively parallel sequencing (MPS) has revolutionised biomedical research and offers enormous capacity for clinical a..

A high-plex PCR approach for massively parallel sequencing

T Nguyen-Dumont, BJ Pope, F Hammet, MC Southey, DJ Park

2013-08-01

Current methods for targeted massively parallel sequencing (MPS) have several drawbacks, including limited design flexibility, exp..

Cross-platform compatibility of Hi-Plex, a streamlined approach for targeted massively parallel sequencing

T Nguyen-Dumont, BJ Pope, F Hammet, M Mahmoodi, H Tsimiklis, MC Southey, DJ Park

2013-01-01

Although per-base sequencing costs have decreased during recent years, library preparation for targeted massively parallel sequenc..