科研黑帮 | Molecular Genetic Anatomy and Risk Profile of Hirschsprung’s Disease

PNAS又来一篇：Gene- and tissue-level interactions in normal gastrointestinal development and Hirschsprung disease

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搜文献，无意间看到一篇相关文章，发现发在顶刊NEJM，本想细细学其精华，没想到看完后犹如晴天霹雳，科研还能这么玩。

Molecular Genetic Anatomy and Risk Profile of Hirschsprung’s Disease

首先看其数据和方法：

exome sequencing of samples from 190 patients of European ancestry and 47 of their affected relatives (7 parents, 12 children, 17 siblings, and 11 second-degree relatives) with diverse phenotypes

外显子测序，190病人样本在这个年代已经属于极少了

analysis of common noncoding variant studies

analysis of copy-number variants

最常规的common NCD variant和CNV研究

four disease-associated SNPs — rs2435357, rs7069590, and rs2506030 in RET and rs11766001 in the SEMA3 gene cluster

选了几个已知的位点来 assessing the effect of common noncoding variants

assessed large copy-number variants (deletions of more than 500 kb and duplications of more than 1 Mb

做的是非常长片段的CNV

To assess the role of a gene in Hirschsprung’s disease, we first used reverse-transcriptase polymerase chain reaction (RT-PCR) to assess its RNA expression in the human embryonic gut at Carnegie stage 22, by which time gut neurogenesis is complete (Fig. S6 in the Supplementary Appendix). Second, we tested gene expression by RNA sequencing and RT-PCR in the developing mouse gut during the equivalent developmental period (embryonic day 10.5) (Fig. S6 in the Supplementary Appendix). Third, we used morpholinos (antisense oligonucleotides) to knock down gene expression in zebrafish embryos at 6 days after fertilization and enumerated the enteric neurons colonizing the gut relative to controls (Fig. S7 in the Supplementary Appendix).

这就是功能验证，我一个dry lab的都觉得过于粗放，能说明什么呢？

STATISTICAL ANALYSIS

样本、研究策略都没有创新，那就统计上来一点吧，可惜还是没有。通篇都是odds ratios, confidence intervals，幼儿园水平。

OK，至此为止，样本量、研究策略、方法都是非常常规的，那你就在结果解读上来点创新吧，说书说得好也行。

看看结果：

COMMON REGULATORY VARIANTS AND RISK

Population Risk of Hirschsprung’s Disease as a Function of RET and SEMA3 Noncoding Risk-Allele Dosage.

核心意思就是，在这两个已知的基因里，risk-allele的dosage会增加risk，也就是odd ratio，这不是废话吗，你不做我都知道。

而且你就选了两个已知的，其他的你都不做了吗？

RISK ASSOCIATED WITH RARE CODING VARIANTS

PATHWAYS AND FUNCTIONAL GROUPS

FREQUENCY OF COPY-NUMBER VARIANTS IN HIRSCHSPRUNG’S DISEASE

DISTRIBUTION OF DIVERSE PATHOGENIC ALLELES

实在没什么好说的，几个简单的表格，做一些最常规的分析，就敢说自己HSCR搞透了。

再加上Complex Simplicity and Hirschsprung’s Disease这个comment，一群黑帮正处于极度的自嗨当中。

“Science envy comes in many flavors, and it is particularly easy to envy those who are privileged to discover simple stories.”

我们嫉妒你，不要搞错了，恶心和鄙视 ≠ 嫉妒

这种水平的研究结果敢透NEJM，NEJM还敢接受，接受了还敢找人写这种comment，你美国做科研的态度也不过如此。

enrichment of CNV is because they put in people that knows that have Down syndrome
and CNV from karyotyping
you don't need an WES to know the enrichment
and those new genes......there is no burden .......
those are mainly from karyotyping and all are super long