T細(xì)胞(TCR)克隆多樣性的指標(biāo)(CPK)

一、CPK是什么

CPK就是一個(gè)衡量，T細(xì)胞(TCR)克隆多樣性的指標(biāo)[Ref1]。它越高就說明文庫大小標(biāo)準(zhǔn)化后的CDR3數(shù)目越多，也就是T細(xì)胞克隆多樣性越強(qiáng)。

Ref1:是這樣描述的We therefore used the number of unique CDR3 calls in each sample normalized by the total read count in the TCR region, which we call clonotypes per thousand (kilo) reads (CPK), as a measure of clonotype diversity (Online Methods).

二、為什么要用CPK

在低的reads覆蓋度，CDR3的數(shù)目近似與reads數(shù)成線性增加的關(guān)系，只要reads的覆蓋度達(dá)不到飽和(一般是超過100 million reads)，distinct CDR3的數(shù)目和reads的數(shù)目比例就不會依賴于序列的文庫大小[Ref1]。所以在多樣性指標(biāo)計(jì)算中，需要校正掉文庫大小這個(gè)因素。

Ref1: 是這樣描述的

At low read coverage, the number of distinct CDR3 sequences increases approximately linearly with read count.

This result suggests that the ratio of distinct CDR3 sequence calls over the number of reads is independent of sequence library size, as long as the read count does not reach the saturation level, which is typically larger than 100 million reads.

三、什么時(shí)候需要用CPK

需要計(jì)算你CDR3的數(shù)目是否達(dá)到飽和狀態(tài)，如果你的數(shù)目和文庫大小有強(qiáng)的線性相關(guān)關(guān)系，那就說明該覆蓋度下的reads未達(dá)到飽和水平[Ref1]，此時(shí)就需要校正掉文庫大小，即需要使用CPK。

(Ref1)Comparing to our observation in Figure 4a, we concluded that the read counts we obtained from RNA-seq data were far from saturation and stayed in the linear phase.

四、怎么計(jì)算CPK(clonotypes per thousand (kilo) reads (CPK))

CPK= (the number of unique CDR3)*1000/( the total read count in the TCR region) [Ref1]

Ref1:是這樣描述的We therefore used the number of unique CDR3 calls in each sample normalized by the total read count in the TCR region, which we call clonotypes per thousand (kilo) reads (CPK), as a measure of clonotype diversity (Online Methods).

附：

Ref1:Landscape of tumor-infiltrating T cell repertoire of human cancers,Nat genetics,2016,27