6 articles Publications

Phylotree 17 available

phylotree17

After exactly 2 years, Phylotree, the “database” behind HaploGrep got updated by Mannis van Oven. Here’s the accompanying publication on Phylotree 17 . The mtDNA tree has now 5,437 haplogroups, which is a growth of over 13% to the previous version. Find out how Phylotree 17 differs for your dataset, by using the updated HaploGrep 2 Version, with the latest mtDNA tree build 17.

 

 

 

1000G Phase 3 mtDNA data available

nature_1000G_phase3

The 1000 Genome Consortium recently released the Phase 3 mitochondrial DNA data of over 2,500 samples for download, besides their papers in Nature, stating:

Mitochondrial chromosome variants are now available for the Phase 3 individuals from our FTP site

Since in the current Version HaploGrep 2 can deal with the VCF file (unzipped), all 2500 samples can be analyzed instantly

New Feature: Tree-based visualisation of haplogroups

phylogenizer_burma

Within the new HaploGrep 2.0 Beta version some new export formats are now supported. One of the most powerful is the export of a phylogenetic tree, representing the current profiles loaded into HaploGrep. This feature generates almost publication-ready  phylogenetic trees. We used them with almost no modification (some color-highlighting in Inkscape) – please see [1].

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Importing VCF file to HaploGrep 2.0

vcf_panes

With the establishment of NGS-Devices and the resulting data flood, new file formats such as FASTQ, SAM, BAM or VCF became de-facto standards in the bioinformatics data world.
Especially the VCF-file containing the variants became of special interest in the user requests lately. There are some python scripts available, that convert a VCF file to a HaploGrep hsd file, as well as a publication with a tool that dedicates itself to this topic. To simplify your life, we decided to implement the VCF file import directly into HaploGrep2. You can give it a try with the 1000 Genome mtDNA VCF file from Phase 1:

1000G Phase 1 VCF File

 

rCRS vs. RSRS vs. HG19 (Yoruba)

It’s not always straight forward when working with the human mitochondrial DNA, even if it comes to the question: “what reference sequence do you use?” There should be just one reference and the questions therefore obsolete – what however is not the case.

Since the first sequencing of the human mitochondrial genome by Anderson et al. in 1981 the length was defined to be 16,569 base pairs naming it Cambridge Reference Sequence. Even if some years later errors in this first sequencing were corrected by Andrews et al. in 1999, (Genbank NC_012920.1) the new revised Cambridge Reference Sequence (rCRS) was kept the same length – although a deletion on 3107 was found, it was kept by introducing an N. So the 3107N is basically a deletion, kept so that the positions on CRS and rCRS are still comparable.
From many aspects, the choice of an european Haplogroup (H2a2a1) being the reference sequence is not the best one. Therefore Behar et al. proclaimed a new reference sequence in 2012 – a hypotetical one – the so called Reconstructed Sapiens Reference Sequence preserving the historical genome annotation numbering, but not starting with an leaf-sequence in the phylogenetic tree as is the case with the rCRS, but with a “mitochondrial Eve” as root. The two base insertion on 523-524 are represented as NN instead of AC, therefore the RSRS has 3 N positions (523N, 524N, 3107N). Mannis, the father of Phylotree made this table showing the differences between rCRS and RSRS.

We didn’t however change to the RSRS, since we agree with Bandelt et al., that an additional reference sequence causes confusion. But there’s yet another mtDNA reference sequence around, you should be aware of – present in GRCh37/ UCSC Hg19 or the older GRCh36/UCSC Hg18

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