只有4篇参考文献的队列研究
注意到这个研究是因为自己也一直在看乳腺癌相关文献，2021年1月新鲜出炉的，标题是：《Prevalence and reclassification of BRCA1 and BRCA2 variants in a large, unselected Chinese Han breast cancer cohort》，链接是：https://link.springer.com/article/10.1186/s13045-020-01010-0
全文短小精悍，就是汇总了课题结果，一个多中心队列：a Chinese multicenter cohort of 21,216 BC patients and 6434 healthy controls. 在这个队列做了 panel-based sequencing served to detect *BRCA1/*2 variants ，汇报一下结果，就是：pathogenic variants was 5.5% (1174/21,216) in BC patients and 1.1% (71/6434) in healthy controls.
当然了，仅仅是发现突变就太小儿科了，起码的注释和分类仍然是要弄的，重要的知识点是ClinVar database (clinvar_20171002.vcf.gz) and ACMG guidelines
- 532 (27.2%) variants are pathogenic,
- 858 (43.8%) are VUS,
- the remaining 568 variants (29.0%) are benign
这样全部筛查到的1958 BRAC1/2 variants 就有了意义。当然了，还可以深入到基因的外显子，功能结构域去讨论这些突变，比如：
- Zinc/Ring finger (green);
- Serine cluster domain (blue);
- BRCT domain (red);
- BRCT (C terminus) (yellow).
让我们来看看，他为什么只有4个参考文献：
其中两个参考文献是中国人的类似的*BRCA1/*2 研究队列：
- Germline mutations in cancer susceptibility genes in a large series of unselected breast cancer patients. Clin Cancer Res. 2017;
- Germline variation in BRCA1/2 is highly ethnic-specific: evidence from over 30,000 Chinese hereditary breast and ovarian cancer patients. Int J Cancer. 2019;
还有一个参考文献是韩国人队列：
- The prevalence and spectrum of BRCA1 and BRCA2 mutations in Korean population: recent update of the Korean Hereditary Breast Cancer (KOHBRA) study. Breast Cancer Res Treat. 2015;
这些都是理所当然的， 甚至如果想把文章内容丰富一点，可以搜罗全世界各地的*BRCA1/*2 队列研究，欧美那边超级多。
不过，最后一篇参考文献就很有意思了，曾经一度刷爆朋友圈：Accurate classification of BRCA1 variants with saturation genome editing. Nature. 2018; 那，为什么引用它呢，我看了看，是We also re-analyzed the 100 variants in 13 exons (2–5 and 15–23) of the BRCA1 genes using a functional assay (saturation genome editing; SGE).
- 55 of the 59 VUS had distinct status in the SGE study:
- 24 (43.6%) were pathogenic,
- 31 (56.4%) were benign.
但即使是他们使用了 saturation genome editing 这个方法，最后仍然是提出来了：there is a need to develop a classification system that categorizes the known variants into pathogenic, VUS, and benign in the Chinese population.
因为他们认为：The biological impact of variants in the literature, allele frequency in the Chinese patients, and the general Chinese population should be incorporated into this classification system.
最后，不得不说，医院科研合作确实是好事，尤其是这样的多个省市多个医院的大队列：During a period from 10-01-2015 to 12-15-2018, we collected 21,216 unselected Chinese BC patients and 6434 healthy controls in 19 medical centers in 11 Chinese provinces
不过，这些变异位点毕竟是来源于测序数据，那么如何从fastq格式的测序数据准确的定位到跟参考基因组不一样的各式各样的变异位点呢？