Owing to rapid advances in the next-generation sequencing technology, the cost of DNA sequencing has been reduced by over several orders of magnitude. However, genomic sequencing of individuals at the population scale...Owing to rapid advances in the next-generation sequencing technology, the cost of DNA sequencing has been reduced by over several orders of magnitude. However, genomic sequencing of individuals at the population scale is still restricted to a few model species due to the huge challenge of constructing libraries for thousands of samples. Meanwhile, pooled sequencing provides a cost-effective alternative to sequencing individuals separately, which could vastly reduce the time and cost for DNA library preparation. Technological improvements, together with the broad range of biological research questions that require large sample sizes, mean that pooled sequencing will continue to complement the sequencing of individual genomes and become increasingly important in the foreseeable future. However, simply mixing samples together for sequencing makes it impossible to identify reads that belongs to each sample. Barcoding technology could help to solve this problem, nonetheless, currently, barcoding every sample is costly especially for large-scale samples. An alternative to barcoding is combinatorial pooled sequencing which employs pooling pattern rather than short DNA barcodes to encode each sample. In combinatorial pooled sequencing, samples are mixed into few pools according to a carefully designed pooling strategy which allows the sequencing data to be decoded to identify the reads that belongs to the sample that are unique or rare in the population. In this review, we mainly survey the experiment design and decoding procedure for the combinatorial pooled sequencing applied in rare variant and rare haplotype carriers screening, complex genome assembling and single individual haplotyping.展开更多
C. Radoux （J. Comput. Appl. Math., 115 （2000） 471-477） obtained a computational formula of Hankel determinants on some classical combinatorial sequences such as Catalan numbers and polynomials, Bell polynomials, H...C. Radoux （J. Comput. Appl. Math., 115 （2000） 471-477） obtained a computational formula of Hankel determinants on some classical combinatorial sequences such as Catalan numbers and polynomials, Bell polynomials, Hermite polynomials, Derangement polynomials etc. From a pair of matrices this paper introduces two kinds of numbers. Using the first kind of numbers we give a unified treatment of Hankel determinants on those sequences, i.e., to consider a general representation of Hankel matrices on the first kind of numbers. It is interesting that the Hankel determinant of the first kind of numbers has a close relation that of the second kind of numbers.展开更多
文摘Owing to rapid advances in the next-generation sequencing technology, the cost of DNA sequencing has been reduced by over several orders of magnitude. However, genomic sequencing of individuals at the population scale is still restricted to a few model species due to the huge challenge of constructing libraries for thousands of samples. Meanwhile, pooled sequencing provides a cost-effective alternative to sequencing individuals separately, which could vastly reduce the time and cost for DNA library preparation. Technological improvements, together with the broad range of biological research questions that require large sample sizes, mean that pooled sequencing will continue to complement the sequencing of individual genomes and become increasingly important in the foreseeable future. However, simply mixing samples together for sequencing makes it impossible to identify reads that belongs to each sample. Barcoding technology could help to solve this problem, nonetheless, currently, barcoding every sample is costly especially for large-scale samples. An alternative to barcoding is combinatorial pooled sequencing which employs pooling pattern rather than short DNA barcodes to encode each sample. In combinatorial pooled sequencing, samples are mixed into few pools according to a carefully designed pooling strategy which allows the sequencing data to be decoded to identify the reads that belongs to the sample that are unique or rare in the population. In this review, we mainly survey the experiment design and decoding procedure for the combinatorial pooled sequencing applied in rare variant and rare haplotype carriers screening, complex genome assembling and single individual haplotyping.
基金the National Natural Science Foundation of China(Grant No.10471016)the Natural Science Foundation of Henan Province(Grant No.0511010300)the Natural Science Foundation of the Education Department of Henan Province(Grant No.200510482001)
文摘C. Radoux （J. Comput. Appl. Math., 115 （2000） 471-477） obtained a computational formula of Hankel determinants on some classical combinatorial sequences such as Catalan numbers and polynomials, Bell polynomials, Hermite polynomials, Derangement polynomials etc. From a pair of matrices this paper introduces two kinds of numbers. Using the first kind of numbers we give a unified treatment of Hankel determinants on those sequences, i.e., to consider a general representation of Hankel matrices on the first kind of numbers. It is interesting that the Hankel determinant of the first kind of numbers has a close relation that of the second kind of numbers.
