DNA mismatch repair is not disrupted in stage 0 colorectal cancer resected using endoscopic submucosal dissection

Nishio

et al. 2021

Preprint

Self Cite

To implement precision oncology, analytical validity as well as clinical validity and utility are important. However, proficiency testing (PT) to assess validity has not yet been systematically performed in Japan. To investigate the quality of next-generation sequencing (NGS) platforms and cancer genome testing prevalent in laboratories, we performed pilot PT using patient samples. We prepared 5 samples from patients with lung or colorectal cancer, extracted genomic DNA from the cancer tissue and peripheral blood, and distributed these to 15 laboratories. Most participating laboratories successfully identified the pathogenic variants, except for two closely located KRAS variants, and 25-bp delins in the EGFR exon 19, not identified by the in vitro diagnostics testing. Conversely, the EGFR L858R variant was successfully identified, and the allele frequency was similar for all the laboratories. A high DNA integrity number led to excellent depth and reliable NGS results. All NGS platforms and bioinformatics pipelines have advantages and disadvantages. We propose the use of a PT program using patient samples to ascertain the quality status of cancer gene testing in laboratories and to ensure that laboratories have sufficient information to develop advancements in precision medicine for cancer.

Section: Additional Analysis Methods For the Pt Samplesmentioning

confidence: 99%

A Pilot Proficiency Testing Study for Assessing Cancer Gene Panel using Patient Samples and Next-generation Sequencing in Japan

Maekawa

Nishio

et al. 2021

Preprint

Self Cite

“…IHC staining IHC was performed as described previously. [24] Staining for the expression of MLH1 protein was performed using 10% formalin xed for 6-48 h at room temperature, and para n-embedded blocks were cut into 4 µm thick serial sections. The slides were dewaxed by heating at 55°C for 30 min, followed by three 5 min washes with xylene.…”

Section: Next-generation Sequencing (Ngs)mentioning

confidence: 99%

Pure somatic pathogenic variation profiles for patients with serrated polyposis syndrome

Hidaka

Iwaizumi

et al. 2021

Preprint

Self Cite

Background The serrated pathway is a distinct genetic/epigenetic mechanism of the adenoma-carcinoma sequence in colorectal carcinogenesis. Although many groups have reported the genetic-phenotypic correlation of serrated lesions (SLs), previous studies regarding the serrated pathway were conducted on patients with SLs that have heterogeneous germline genetic backgrounds. We aimed to compare pure somatic genetic profiles among SLs within identical patients with SPS as a homogenous germline background. Methods We analysed SLs from one patient with SPS (Case #1) and compared DNA variant profiles using targeted DNA multigene panels via NGS among the patient’s hyperplastic polyp (HP), three sessile serrated lesions (SSLs), and one traditional serrated adenoma (TSA), in addition to leucocytes as a germline variant, and separately analysed three SSLs and one tubular adenoma (TA) within another patient with SPS (Case #2). Results In two patients, no germline pathogenic variant was observed, and a known pathogenic variant of BRAF (c.1799T > A, p.Val600Glu) was observed in one TSA and one SSL in Case #1, while three SSLs exhibited the BRAF variant in Case #2. Further, the genetic profile of TA is consistent with the adenoma-carcinoma sequence pathway profile and distinct from that of the other SLs within the same patient with SPS. Conclusions These findings of pure somatic genetic variant profiles among SLs with identical germline genetic background support the previous results analysed among SLs with heterogeneous germline genetic backgrounds.

Precision cancer genome testing needs proficiency testing involving all stakeholders

Maekawa

Nishio

et al. 2022

Sci Rep

To implement precision oncology, analytical validity as well as clinical validity and utility are important. However, proficiency testing (PT) to assess validity has not yet been systematically performed in Japan. To investigate the quality of next-generation sequencing (NGS) platforms and cancer genome testing prevalent in laboratories, we performed pilot PT using patient samples. We prepared genomic DNA from the cancer tissue and peripheral blood of 5 cancer patients and distributed these to 15 laboratories. Most participating laboratories successfully identified the pathogenic variants, except for two closely located KRAS variants and 25 bp delins in EGFR. Conversely, the EGFR L858R variant was successfully identified, and the allele frequency was similar for all the laboratories. A high DNA integrity number led to excellent depth and reliable NGS results. By conducting this pilot study using patient samples, we were able to obtain a glimpse of the current status of cancer genome testing at participating laboratories. To enhance domestic cancer genome testing, it is important to conduct local PT and to involve the parties concerned as organizers and participants.