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We work with a specific copy pipeline equipped with different copy modes which are all possible combinations of mono/color, text/mix/picture/photo, and periodic/stochastic.
The genome sequences of the six individuals were used to identify individual specific copy number variations as compared to NCBI Build 37. Table 5 shows the distribution of observed CNVs in MZ twins representing the two families.
Many possible candidates have been proposed, including specific copy number variations, NOTCH4, and histone protein loci.
Regions of allelic imbalance were determined using the allele specific copy number (AsCN) function of Partek.
Further, the transition probability depends on the state specific copy number.
We also detected a high percentage of specific copy number alterations, like DDR2, PYGO2 and SCYL3.
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Here, we introduce Weaver, an algorithm for the quantification and analysis of allele-specific copy numbers of SVs.
However, existing methods can identify either SVs or allele-specific copy number alterations but not both simultaneously, which provides a limited view of cancer genome structure.
Weaver uses a Markov random field to estimate joint probabilities of allele-specific copy numbers of SVs and their inter-connectivity based on paired-end whole-genome sequencing data.
We apply Weaver to generate allele-specific copy numbers of SVs for MCF-7 and HeLa cell lines and identify recurrent SV patterns in 44 TCGA ovarian cancer whole-genome sequencing datasets.
However, of another 15 genes previously reported as exhibiting ALS-specific copy number variation, only four exhibited copy number variation in this study.
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