Open Access Methodology article

Identification of medium-sized genomic deletions with low coverage, mate-paired restricted tags

Qiang Gong12, Yong Tao1, Jian-Rong Yang3, Jun Cai1, Yunfei Yuan4, Jue Ruan1, Jin Yang5, Hailiang Liu3, Wanghua Li12, Xuemei Lu15, Shi-Mei Zhuang3, San Ming Wang6 and Chung-I Wu17*

Author Affiliations

1 Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P.R. China

2 University of Chinese Academy of Sciences, Beijing, P.R. China

3 Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, P.R. China

4 Department of Hepatobiliary Oncology, Cancer Center, Sun Yat-sen University, Guangzhou, P.R. China

5 Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P.R. China

6 Department of Genetics, Cell Biology & Anatomy, College of Medicine, University of Nebraska Medical Center, Nebraska, USA

7 Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA

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BMC Genomics 2013, 14:51  doi:10.1186/1471-2164-14-51

Published: 24 January 2013

Additional files

Additional file 1: Table S1:

Cutting frequencies on reference HG18 of different restriction recognizing sequence.

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Additional file 2: Figure S1:

Ditag coverage by chromosomes. A) Restriction sites covered by the experimental ditags corresponding to the reference; B) Genomic regions covered by the restriction fragments tagged by the experimental ditags. Figure S2. Venn diagram of A) the number of Ref-Ditags covered by the two libraries; B) the deletions identified using ditags from Lib1, Lib2 and the combined data. Figure S3. A 3075-bp heterozygous deletion that skips 5 consecutive restriction sites on chromosome 17. Ditags were used to design a pair of primers to amplify the breakpoint-containing sequences. The results showed two bands representing the reference and mutant bands, respectively. The breakpoint sequence was identified by direct Sanger sequencing. Figure S4. Flow-chart of the ditag library construction process. Figure S5. Nick-translation distances of the two libraries inferred from the reads alignment.

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Additional file 3: Table S2:

A list of the identified medium-sized deletions.

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Addtional file 4:

A package of scripts and related programs conducting the analysis.

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Additional file 5: Table S3:

Primers used for validation.

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