Tag: Control-FREEC

Shallow whole genome sequencing approach to detect Homologous Recombination Deficiency in the PAOLA-1/ENGOT-OV25 phase-III trial

Polak P, Kim J, Braunstein LZ, Karlic R, Haradhavala NJ, Tiao G, et al. A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer. Nat Genet. 2017;49:1476–86. Article  CAS  PubMed  PubMed Central  Google Scholar  Birkbak NJ, Wang ZC, Kim JY, Eklund AC, Li Q, Tian R, et…

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sarek: Introduction

Introduction nf-core/sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any species with a reference genome. Sarek can also handle tumour / normal pairs and could include additional relapses. The pipeline is built using…

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Segmentation fault error in CONTROL-FREEC

Hi, I am trying to run CONTROL-FREEC on diploid yeast samples to detect CNVs on a department cluster. The config file looks like this: [general] chrLenFile = yeast_chr.len ploidy = 2 window = 150000 #breakPointThreshold = -.002; #coefficientOfVariation = 0.062 chrFiles = /net/smith/vol1/home/student/FREEC-11.6b/data/test_sludge/yeast_files outputDir = /net/smith/vol1/home/student/FREEC-11.6b/data/test_sludge/output #degree=3 [sample] mateFile =…

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Whole-genome doubling drives oncogenic loss of chromatin segregation

Cell culture hTERT-RPE-1 WT and hTERT RPE-1 TP53−/− (46, XX)27 cells were a gift from J. Korbel. The cells were grown in DMEM/F-12, GlutaMAX (10565018) supplemented with 10% FBS (Thermo Fisher Scientific, 10270106) and 1% antibiotic–antimycotic (Thermo Fisher Scientific, 15240062). CP-A (KR-42421) (47, XY) cells were purchased from the American Type…

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Control-FREEC output

Control-FREEC output 0 Hello everybody, I’m using the tool Control-FREEC to evaluate the CNVs in my data, but I have some doubts about the _ratio.txt file in output. As far as I understood by both the paper and the documentation, this file should report the ratio (that, if I’m correct,…

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iPSCs derived from infertile men carrying complex genetic abnormalities can generate primordial germ-like cells

Patients and controls The patient 1 was 38 years old and consulted for infertility after he and his partner had been trying to conceive for 2 years. The patient was the first child of unrelated parents, and he had four brothers and five sisters whose fertility status could not be determined…

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CNV calling for wgs of S. pombe

CNV calling for wgs of S. pombe 0 Hi, Can anyone help to do CNV calling of WGS data of S.Pombe? I have 1 normal sample and 3 samples treated with a suppressor. I used Control-FREEC but did not get the right result. Can anyone help, how to do germline…

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A genomic mutation spectrum of collecting duct carcinoma in the Chinese population

This article was originally published here BMC Med Genomics. 2022 Jan 3;15(1):1. doi: 10.1186/s12920-021-01143-2. ABSTRACT BACKGROUND: Renal collecting duct carcinoma (CDC) is a rare and lethal subtype of renal cell carcinoma (RCC). The genomic profile of the Chinese population with CDC remains unclear. In addition, clinical treatments are contradictory. In…

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