Neumeier Yaara, Raz Ofir, Tao Liming, Marx Zipora, Shapiro Ehud
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.
Methods Mol Biol. 2025;2886:23-45. doi: 10.1007/978-1-0716-4310-5_2.
The human genome is composed of distinct genomic regions that are susceptible to various types of somatic mutations. Among these, Short Tandem Repeats (STRs) stand out as the most mutable genetic elements. STRs are short repetitive polymorphic sequences, predominantly situated within noncoding sectors of the genome. The intrinsic repetition characterizing these sequences makes them highly mutable in vivo. Consequently, this characteristic provides the chance to unravel the natural developmental history of human viable cells retrospectively. However, STRs also introduce stutter noise in vitro amplification, which makes their analysis challenging. Here we describe our integrated biochemical-computational platform for single-cell lineage analysis. It consists of a pipeline whose inputs are single cells and whose output is a lineage tree of input cells.
人类基因组由不同的基因组区域组成，这些区域易受各种类型的体细胞突变影响。其中，短串联重复序列（STR）是最易发生突变的遗传元件。STR是短的重复多态性序列，主要位于基因组的非编码区域。这些序列的固有重复特性使其在体内具有高度的可变性。因此，这一特性为追溯人类活细胞的自然发育历史提供了机会。然而，STR在体外扩增中也会引入拖尾噪声，这使得对其进行分析具有挑战性。在此，我们描述了用于单细胞谱系分析的集成生化计算平台。它由一个流程组成，其输入是单细胞，输出是输入细胞的谱系树。
