scholarly journals Correction to: APC germline variant analysis in the adenomatous polyposis phenotype in Japanese patients

Author(s):  
Misato Takao ◽  
Tatsuro Yamaguchi ◽  
Hidetaka Eguchi ◽  
Takeshi Yamada ◽  
Yasushi Okazaki ◽  
...  
Author(s):  
Misato Takao ◽  
Tatsuro Yamaguchi ◽  
Hidetaka Eguchi ◽  
Takeshi Yamada ◽  
Yasushi Okazaki ◽  
...  

Author(s):  
Sen Zhao ◽  
Oleg Agafonov ◽  
Abdulrahman Azab ◽  
Tomasz Stokowy ◽  
Eivind Hovig

AbstractAdvances in next-generation sequencing technology has enabled whole genome sequencing (WGS) to be widely used for identification of causal variants in a spectrum of genetic-related disorders, and provided new insight into how genetic polymorphisms affect disease phenotypes. The development of different bioinformatics pipelines has continuously improved the variant analysis of WGS data, however there is a necessity for a systematic performance comparison of these pipelines to provide guidance on the application of WGS-based scientific and clinical genomics. In this study, we evaluated the performance of three variant calling pipelines (GATK, DRAGEN™ and DeepVariant) using Genome in a Bottle Consortium, “synthetic-diploid” and simulated WGS datasets. DRAGEN™ and DeepVariant show a better accuracy in SNPs and indels calling, with no significant differences in their F1-score. DRAGEN™ platform offers accuracy, flexibility and a highly-efficient running speed, and therefore superior advantage in the analysis of WGS data on a large scale. The combination of DRAGEN™ and DeepVariant also provides a good balance of accuracy and efficiency as an alternative solution for germline variant detection in further applications. Our results facilitate the standardization of benchmarking analysis of bioinformatics pipelines for reliable variant detection, which is critical in genetics-based medical research and clinical application.


2017 ◽  
Vol 05 (03) ◽  
pp. E137-E145 ◽  
Author(s):  
Keiko Nakamura ◽  
Satoru Nonaka ◽  
Takeshi Nakajima ◽  
Tatsuo Yachida ◽  
Seiichiro Abe ◽  
...  

Abstract Background and study aims Familial adenomatous polyposis (FAP) is an autosomal dominant syndrome caused by a germline mutation in the adenomatous polyposis coli (APC) gene, characterized by the presence of more than 100 adenomatous polyps in the colorectum. The upper gastrointestinal tract is an extracolonic site for malignancy in patients with FAP. The frequency of death in Japanese patients with FAP because of gastric cancer is 2.8 % and that because of colon cancer is 60.6 %. Few studies have reported upper gastrointestinal diseases in patients with FAP. In the present study, we investigated the clinical outcomes of patients with FAP diagnosed with gastric neoplasms. Patients and methods We enrolled 80 patients with FAP who underwent esophagogastroduodenoscopy from October 1997 to December 2011. We investigated patient characteristics, endoscopic findings of gastric lesions, treatment outcomes, and long-term courses. Results Fundic gland polyposis was observed in 51 patients (64 %) and gastric neoplasms in 22 patients (28 %), including 20 with non-invasive and 2 with invasive neoplasm. Of the 26 neoplasms, 11 were treated by endoscopic resection (ER) and 4 by surgical resection. Metachronous gastric neoplasms were observed in 7 patients (15 lesions) and treated by ER, except for in 1 patient. No patients died of gastric lesions during a median follow-up period of 6.5 years (range, 0 – 14). Conclusion Because gastric lesions including gastric cancers in patients with FAP did not cause any deaths, they can be considered to have favorable prognoses. Early detection of gastric neoplasms through an appropriate follow-up interval may have contributed to these good outcomes.


2017 ◽  
Vol 51 (5) ◽  
pp. 407-411 ◽  
Author(s):  
Tatsuo Yachida ◽  
Takeshi Nakajima ◽  
Satoru Nonaka ◽  
Keiko Nakamura ◽  
Haruhisa Suzuki ◽  
...  

2008 ◽  
Vol 73 (6) ◽  
pp. 545-553 ◽  
Author(s):  
R Yanaru-Fujisawa ◽  
T Matsumoto ◽  
Y Ushijima ◽  
M Esaki ◽  
M Hirahashi ◽  
...  

2020 ◽  
Author(s):  
Rika Kasajima ◽  
Rui Yamaguchi ◽  
Eigo Shimizu ◽  
Yoshinori Tamada ◽  
Atsushi Niida ◽  
...  

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