Description

This track shows structural variants (SVs) identified by Oxford Nanopore long-read sequencing of 333 Japanese individuals from the Tohoku Medical Megabank (ToMMo) project. The 333 individuals form 111 parent-offspring trios, enabling Mendelian consistency checks on the SV calls. Activated T lymphocytes were used as a source of high-molecular-weight DNA for nanopore sequencing at a median coverage of 22.2x with an N50 read length of 25.8 kb.

The dataset contains 74,201 SVs (37,981 deletions and 36,220 insertions), merged across individuals using SURVIVOR v1.0.6. Over 95% of the SVs are concordant with Mendelian inheritance in the trio families.

Display Conventions and Configuration

Items are colored by SV type:

• Deletions (DEL) - red
• Insertions (INS) - blue

Filters are available for SV type, SV length, and allele frequency. For insertions, the item is placed at the insertion site with a width of 1 bp; for deletions, the item spans the deleted region.

The detail page for each item shows:

• Allele Frequency: fraction of alleles carrying this variant (based on 444 alleles from 222 unrelated parents)
• Allele Count / Allele Number: number of variant alleles and total alleles genotyped
• Mendelian Error Rate: fraction of trio families showing inheritance errors for this variant
• Families with Errors / Families Genotyped: number of families with Mendelian errors and total families with complete genotype calls

Methods

Oxford Nanopore sequencing was performed on genomic DNA extracted from activated T lymphocytes of 333 individuals (111 trios) from the Tohoku Medical Megabank (ToMMo) cohort. SV calling was performed with Sniffles on each sample, and calls were merged across individuals with SURVIVOR v1.0.6 using a maximum distance of 1 kbp. Allele frequencies were computed from 222 unrelated parents (excluding offspring to avoid double-counting). Mendelian error rates were calculated by checking transmission consistency within each trio family.

Data Access

Source data is available from the jMorp data portal (ToMMo Japanese Multi Omics Reference Panel).

Credits

Thanks to the Tohoku Medical Megabank Organization for making their structural variant calls publicly available through the jMorp data portal.

References

Otsuki A, Okamura Y, Ishida N, Tadaka S, Takayama J, Kumada K, Kawashima J, Taguchi K, Minegishi N, Kuriyama S et al. Construction of a trio-based structural variation panel utilizing activated T lymphocytes and long- read sequencing technology. Commun Biol. 2022 Sep 20;5(1):991. PMID: 36127505; PMC: PMC9489684