On the Minimum Copy Number Generation Problem in Cancer Genomics

Qingge, Letu; He, Xiaozhou; Liu, Zhihui; Zhu, Binhai

doi:10.1145/3233547.3233586

Cited by 8 publications

(8 citation statements)

References 28 publications

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“…While this level of resolution provides more power for inferring the actual CNAs, especially large-scale ones that span long genomic regions (e.g., whole-genome duplication), inferences at this level quickly become intractable. Mathematical models and algorithms for genome rearrangement problems in the presence of duplication have been introduced, e.g., [80][81][82][83], some of which are being studied in the context of cancer genomics. However, these models are mostly "gene centric, " that is, they assume loci in the genome have been delineated and number of copies, as well as gene order within each genome, are unknown.…”

Section: Evolutionary Modeling and Analysis Of Cnasmentioning

confidence: 99%

Methods for copy number aberration detection from single-cell DNA-sequencing data

et al. 2020

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Copy number aberrations (CNAs), which are pathogenic copy number variations (CNVs), play an important role in the initiation and progression of cancer. Single-cell DNA-sequencing (scDNAseq) technologies produce data that is ideal for inferring CNAs. In this review, we review eight methods that have been developed for detecting CNAs in scDNAseq data, and categorize them according to the steps of a seven-step pipeline that they employ. Furthermore, we review models and methods for evolutionary analyses of CNAs from scDNAseq data and highlight advances and future research directions for computational methods for CNA detection from scDNAseq data.

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Section: Evolutionary Modeling and Analysis Of Cnasmentioning

confidence: 99%

Methods for copy number aberration detection from single-cell DNA-sequencing data

et al. 2020

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“…Qingge et al proved that the MCNG problem is NP-hard when all the duplications are restricted to be tandem [12]. In the next section, we prove that this problem is not only NP-hard, but also NP-hard to approximate within any constant factor.…”

Section: Definitionmentioning

confidence: 73%

“…In [12], another fundamental problem was proposed. The motivation is that in the early stages of cancer, when large numbers of endoreduplications are still rare, genome sequencing is still possible.…”

Section: Introductionmentioning

confidence: 99%

“…In this paper, we present two streams of results. The first is the negative results on two open problems regarding the computational complexity of the Minimum Copy Number Generation (MCNG) problem posed by Qingge et al in 2018. The Minimum Copy Number Generation (MCNG) is defined as follows: given a string S over a gene set Σ (with |Σ| = n) and a CNP C, compute a string T from S, with the minimum number of segmental duplications and deletions, such that cnp(T ) = C. It was shown by Qingge et al.…”

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confidence: 99%

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Genomic Problems Involving Copy Number Profiles: Complexity and Algorithms

Lafond,

Zhu,

Zou

2020

Preprint

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Recently, due to the genomic sequence analysis in several types of cancer, the genomic data based on copy number profiles (CNP for short) are getting more and more popular. A CNP is a vector where each component is a non-negative integer representing the number of copies of a specific gene or segment of interest. The motivation is that in the late stage of certain types of cancer, the genomes are progressing rapidly by segmental duplications and deletions hence obtaining the exact sequences is becoming more difficult. Instead, in this case, the number of copies of important genes can be predicted from expression analysis and carries important biological information. Therefore, a lot of research have been started to analyze the genomic data represented in CNP's.

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“…The TD distance is one of the many ways of comparing two genomes represented as strings in computational biology -other notable examples include breakpoint [12] and transpositions distances, the latter having recently been shown NP-hard in a celebrated paper of Bulteau et al [3]. The TD distance has itself received special attention recently, owing to its role in cancer evolution [22].…”

Section: Introductionmentioning

confidence: 99%

The Tandem Duplication Distance is NP-hard

Lafond,

Zhu,

Zou

2019

Preprint

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In computational biology, tandem duplication is an important biological phenomenon which can occur either at the genome or at the DNA level. A tandem duplication takes a copy of a genome segment and inserts it right after the segment -this can be represented as the string operation AXB ⇒ AXXB. Tandem exon duplications have been found in many species such as human, fly or worm, and have been largely studied in computational biology. The Tandem Duplication (TD) distance problem we investigate in this paper is defined as follows: given two strings S and T over the same alphabet, compute the smallest sequence of tandem duplications required to convert S to T . The natural question of whether the TD distance can be computed in polynomial time was posed in 2004 by Leupold et al. and had remained open, despite the fact that tandem duplications have received much attention ever since. In this paper, we prove that this problem is NP-hard. We further show that this hardness holds even if all characters of S are distinct. This is known as the exemplar TD distance, which is of special relevance in bioinformatics. One of the tools we develop for the reduction is a new problem called the Cost-Effective Subgraph, for which we obtain W[1]-hardness results that might be of independent interest. We finally show that computing the exemplar TD distance between S and T is fixed-parameter tractable. Our results open the door to many other questions, and we conclude with several open problems.

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On the Minimum Copy Number Generation Problem in Cancer Genomics

Cited by 8 publications

References 28 publications

Methods for copy number aberration detection from single-cell DNA-sequencing data

Methods for copy number aberration detection from single-cell DNA-sequencing data

Genomic Problems Involving Copy Number Profiles: Complexity and Algorithms

The Tandem Duplication Distance is NP-hard

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