Phased Genotyping-by-Sequencing Enhances Analysis of Genetic Diversity and Reveals Divergent Copy Number Variants in Maize

Abstract High-throughput sequencing (HTS) of reduced representation genomic libraries has ushered in an era of genotyping-by-sequencing (GBS), where genome-wide genotype data can be obtained for nearly any species. However, there remains a need for imputation-free GBS methods for genotyping large samples taken from heterogeneous populations of heterozygous individuals. This requires that a number of issues encountered with GBS be considered, including the sequencing of nonoverlapping sets of loci across multiple GBS libraries, a common missing data problem that results in low call rates for markers per individual, and a tendency for applicability only in inbred line samples with sufficient linkage disequilibrium for accurate imputation. We addressed these issues while developing and validating a new, comprehensive platform for GBS. This study supports the notion that GBS can be tailored to particular aims, and using Zea mays our results indicate that large samples of unknown pedigree can be genotyped to obtain complete and accurate GBS data. Optimizing size selection to sequence a high proportion of shared loci among individuals in different libraries and using simple in silico filters, a GBS procedure was established that produces high call rates per marker (>85%) with accuracy exceeding 99.4%. Furthermore, by capitalizing on the sequence-read structure of GBS data (stacks of reads), a new tool for resolving local haplotypes and scoring phased genotypes was developed, a feature that is not available in many GBS pipelines. Using local haplotypes reduces the marker dimensionality of the genotype matrix while increasing the informativeness of the data. Phased GBS in maize also revealed the existence of reproducibly inaccurate (apparent accuracy) genotypes that were due to divergent copy number variants (CNVs) unobservable in the underlying single nucleotide polymorphism (SNP) data.

Download Full-text

Assessing the Role of Copy Number Variants in Prostate Cancer Risk and Progression using a Novel Genome-Wide Screening Method

10.21236/ada568305 ◽

2012 ◽

Author(s):

Donna Lehman ◽

August Blackburn ◽

Robin Leach

Keyword(s):

Prostate Cancer ◽

Cancer Risk ◽

Copy Number ◽

Screening Method ◽

Copy Number Variants ◽

Prostate Cancer Risk ◽

Genome Wide

Download Full-text

Detection and characterization of copy number variants based on whole-genome sequencing by DNBSEQ platforms

10.1101/786962 ◽

2019 ◽

Author(s):

Junhua Rao ◽

Lihua Peng ◽

Fang Chen ◽

Hui Jiang ◽

Chunyu Geng ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Copy Number ◽

Copy Number Variants ◽

Copy Number Variant ◽

Whole Genome ◽

Genome Wide ◽

Wide Range ◽

Distribution Sensitivity ◽

Cnv Detection

AbstractBackgroundNext-generation sequence (NGS) has rapidly developed in past years which makes whole-genome sequencing (WGS) becoming a more cost- and time-efficient choice in wide range of biological researches. We usually focus on some variant detection via WGS data, such as detection of single nucleotide polymorphism (SNP), insertion and deletion (Indel) and copy number variant (CNV), which playing an important role in many human diseases. However, the feasibility of CNV detection based on WGS by DNBSEQ™ platforms was unclear. We systematically analysed the genome-wide CNV detection power of DNBSEQ™ platforms and Illumina platforms on NA12878 with five commonly used tools, respectively.ResultsDNBSEQ™ platforms showed stable ability to detect slighter more CNVs on genome-wide (average 1.24-fold than Illumina platforms). Then, CNVs based on DNBSEQ™ platforms and Illumina platforms were evaluated with two public benchmarks of NA12878, respectively. DNBSEQ™ and Illumina platforms showed similar sensitivities and precisions on both two benchmarks. Further, the difference between tools for CNV detection was analyzed, and indicated the selection of tool for CNV detection could affected the CNV performance, such as count, distribution, sensitivity and precision.ConclusionThe major contribution of this paper is providing a comprehensive guide for CNV detection based on WGS by DNBSEQ™ platforms for the first time.

Download Full-text

RefCNV: Identification of Gene-Based Copy Number Variants Using Whole Exome Sequencing

Cancer Informatics ◽

10.4137/cin.s36612 ◽

2016 ◽

Vol 15 ◽

pp. CIN.S36612 ◽

Cited By ~ 3

Author(s):

Lun-Ching Chang ◽

Biswajit Das ◽

Chih-Jian Lih ◽

Han Si ◽

Corinne E. Camalier ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Copy Number ◽

Copy Number Variants ◽

Estimation Methods ◽

Single Nucleotide Variants ◽

False Positive Error ◽

Reference Set ◽

Genome Wide ◽

Whole Exome

With rapid advances in DNA sequencing technologies, whole exome sequencing (WES) has become a popular approach for detecting somatic mutations in oncology studies. The initial intent of WES was to characterize single nucleotide variants, but it was observed that the number of sequencing reads that mapped to a genomic region correlated with the DNA copy number variants (CNVs). We propose a method RefCNV that uses a reference set to estimate the distribution of the coverage for each exon. The construction of the reference set includes an evaluation of the sources of variability in the coverage distribution. We observed that the processing steps had an impact on the coverage distribution. For each exon, we compared the observed coverage with the expected normal coverage. Thresholds for determining CNVs were selected to control the false-positive error rate. RefCNV prediction correlated significantly ( r = 0.96–0.86) with CNV measured by digital polymerase chain reaction for MET (7q31), EGFR (7p12), or ERBB2 (17q12) in 13 tumor cell lines. The genome-wide CNV analysis showed a good overall correlation (Spearman's coefficient = 0.82) between RefCNV estimation and publicly available CNV data in Cancer Cell Line Encyclopedia. RefCNV also showed better performance than three other CNV estimation methods in genome-wide CNV analysis.

Download Full-text

Spontaneous mutations in maize pollen are frequent in some lines and arise mainly from retrotranspositions and deletions

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1903809116 ◽

2019 ◽

Vol 116 (22) ◽

pp. 10734-10743 ◽

Cited By ~ 13

Author(s):

Hugo K. Dooner ◽

Qinghua Wang ◽

Jun T. Huang ◽

Yubin Li ◽

Limei He ◽

...

Keyword(s):

Copy Number ◽

Large Scale ◽

High Throughput Sequencing ◽

Ltr Retrotransposons ◽

Spontaneous Mutations ◽

Maize Pollen ◽

Genome Wide ◽

Autonomous Element ◽

Low Copy Number ◽

Female Germline

While studying spontaneous mutations at the maizebronze(bz) locus, we made the unexpected discovery that specific low-copy number retrotransposons are mobile in the pollen of some maize lines, but not of others. We conducted large-scale genetic experiments to isolate newbzmutations from severalBzstocks and recovered spontaneous stable mutations only in the pollen parent in reciprocal crosses. Most of the new stablebzmutations resulted from either insertions of low-copy number long terminal repeat (LTR) retrotransposons or deletions, the same two classes of mutations that predominated in a collection of spontaneouswxmutations [Wessler S (1997)The Mutants of Maize, pp 385–386]. Similar mutations were recovered at the closely linkedshlocus. These events occurred with a frequency of 2–4 × 10−5in two lines derived from W22 and in 4Co63, but not at all in B73 or Mo17, two inbreds widely represented in Corn Belt hybrids. Surprisingly, the mutagenic LTR retrotransposons differed in the active lines, suggesting differences in the autonomous element make-up of the lines studied. Some active retrotransposons, likeHopscotch,Magellan, andBs2, aBs1variant, were described previously; others, likeFotoandFocouin 4Co63, were not. By high-throughput sequencing of retrotransposon junctions, we established that retrotranposition ofHopscotch,Magellan, andBs2occurs genome-wide in the pollen of active lines, but not in the female germline or in somatic tissues. We discuss here the implications of these results, which shed light on the source, frequency, and nature of spontaneous mutations in maize.

Download Full-text