cluster、SV和CV相关算法

cluster

为什么关注聚类**

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k-means

原理

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相关内容

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• Start with suitable choices of K cluster mean-vectors. Then iterate the following two steps：

• For each object, find the closest mean vector and assign the the object to the corresponding cluster.

• For each cluster, update its mean vector according to the current assignments.

• Convergence is easy stop when cluster assignment no longer changes

• The choice of initial values is more difficult

Hierarchical Clustering

Produce a nested sequence of clusters, a tree, also called Dendrogram

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结构变异Genomic alterations

癌症中尤为明显

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适合用circos来展示

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SV

Mechanisms of SVs

• NAHR - non-allelic homologous recombination
• NHEJ - joining of DNA double-strand breaks without extensive sequence homology by ligation of DNA ends
• Breakage-fusion-bridge (BFB)
• Telomere loss or double-strand breakage creates an unprotected DNA end
• Ligation of broken chromatid ends connects the two sister chromatids
• Chromothripsis： A large number of genomic rearrangements have been acquired in a single catastrophic event

用高通量数据short reads来探测SV

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一些具体方法（可参考原始文献）

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通过以下四个信息来进行预测

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• read pairs
• read depth
• split reads
• and also assembly of the reads into contig

Copy number alterations （CV）

Use network flow to find out the traversal in the genome with CNAs

• Aneuploidy 非整倍体，染色体中出现非整倍体的变化，癌症中很常见

• Quantify allele-specific SVs and CNAs 软件：Weaver

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