In addition, I release under a CC0 license the following sequence-derived data from OGT’s services: a) the aligned and processed BAM file, b) the BAM file index and c) the compressed VCF file. The BAM file (.bam) is the binary version of a tab-delimited text file that contains sequence alignment data. The BAM file index (.bai) provides fast random access to the BAM file. The compressed VCF file (.vcf.gz) describes variant calls in text format. These format types are industry standard and can be used in a variety of research contexts involving genome visualization and analysis.

Looking at the summary metrics in OGT’s report, my personal exome produces:

• 30,702 variations to the reference genome (GRCh37)
• 5,565 non synonymous coding variations with consequences
• A minimum of 61.42% of the on-target regions, covered with a depth of at least 20x (remember that this data was sequenced by the BGI).
• A total of 2.54 Gigabases of sequence data read and aligned at high quality.

Figure 1 is a screenshot of the OGT report showing the summary of all variants identified, including those in dbSNP release 132.

Figure 2 summarizes all novel variants identified by OGT, filtering those in dbSNP release 132.

Download of BAM and VCF Files

You are allowed to use my personal exome’s BAM and VCF files under a completely free license CC0. You can add this data to any database or resource with no need for attribution. Any usage or finding derived from this data communicated back to me will be shared (if considered noteworthy) through this blog or publication, with due attribution or request for coathorship in papers.

• Aligned BAM file download
• Index BAM file download
• VCF file download

In this interview I talk about my experiences in analyzing my genome and the genomes of my family. Here I also introduce the motivation and future plans for the analysis of my personal exome (i.e. all coding regions in my genome).

Some further information regarding my family experience of personal genomics can be found in a recent publication.

What is an exome?

An exome is the ~1% of my genome that encodes for proteins.

Why do I release my personal exome?

When my family and myself made our genotypes available through the Internet, we immediately received results from researchers around the world who took our data for analysis and came back with interesting results. As a result of this, we have been able to learn much about ourselves. I have reported this in a previous entry on this blog entitled “Benefits for Publishing Family Genomes on the Internet“. I now follow the same principle: if I make my exome available for people to analyse it, I can expect that some researchers may come back with interesting results.

What data do I actually release?

I release my 4 FastQ files that were given to me by my sequencing provider. This is the same kind of information that 23andMe gives in their current exome analysis offer. This information basically consists of raw reads that need to be aligned to a reference assembly. Once aligned, interesting variation data can be inferred.

What do I ask in return?

Nothing. I do appeal though to the good will of potential users to report back to me anything interesting they might find.

How big are the files?

They are huge. On average they are about 0.6 Gb per file and I have 4 of these. That means that it can take several hours for each file to be downloaded. Be patient!

Where can I get them?

Here:

1. File 1
2. File 2
3. File 3
4. File 4

How did I get my personal exome sequenced?

Completely independently. If you want to know the story on how I did it, please refer to my blog entries “Getting My Genome Sequencing Done” Part I and Part II. As it is implied there, I managed to get my personal genome sequenced by knocking on quite a few doors and then finding someone who would sponsor me to do so. In fact, part of this exercise’s aim was to prove that it is possible now a days for ordinary citizens to get their genomes sequenced if they so wish.

In order to have the most up-to-date version for the Human Genome set of genes and features sometimes it is necessary to convert from one assembly to another. In the past I have written a tutorial on how to remap from NCBI36 to GRCh37 human assemblies using liftOver. In this tutorial I present a simple step-by-step guide for feature remapping using NCBI’s remapping tool.

Important:

Please make sure you know in advance the assembly to which your aberration data is currently mapped to. If by mistake you remap an aberration already in GRCh37 to GRCh37 you will get new coordinates for the region mapped to the wrong coordinates.

The NCBI provides a web facility to convert coordinates from one assembly into another. To convert coordinates using their genome remapping service do the following:

1. Make sure that your data is in BED format,  e.g. “chr3            100000 999990 myId0000123” -> CNV aberration in NCBI36/hg18

• Please note that each field is separated by a tab and each line by a character return. Please follow this strictly or the remapping tool may throw an error.
• Add as many lines as aberrations you would like to remap

1. Go to the NCBI Remap page:

• http://www.ncbi.nlm.nih.gov/genome/tools/remap/

1. Select “Organism for source data” Homo Sapiens, “Source Assembly” NCBI36 (hg18) and “Target Assembly” GRCh37 (hg19)
2. Please leave all “Remapping Options” (Minimum ratio of bases that must remap, etc) with default values
3. Select for “Input format” BED, “Output format” Same as input
4. Paste your aberration in the input box where it says “Paste data here” and hit submit at the bottom of the page
5. Wait until results are returned
6. To retrieve results download “Mapping Report”, which is in excel format or alternatively Mapping report Sample in the results page

Please note that your aberration may remap to more than one location. I recommend that you manually check the coordinates and select the most appropriate of the doubly remapped aberration in the new assembly. Please also note that your aberration may not remap because the region is partially or entirely deleted in the new assembly or split in GRCh37. In this case I recommend that you use another start or end point position, maybe use the start/end of alternative probes until you find a region where it maps.

Another possibility could be to look at the genes for the region in the old assembly and select a region in GRCh37 that includes the same genes as in NCBI36. Each of these solutions requires careful deliberation and may not be applicable to your particular case (e.g. genes in different chromosomes would not allow remapping based on genes).

The case study paper is an invited contribution for the Journal of Genetic Counseling in a special issue on Direct-To-Consumer (DTC) genetic testing. This paper describes the journey I went through with my family when we all embarked into analysing our personal genomes via a DTC genetic testing company. I believe my experiences could be related to many other people in the world as they gain access to this technology. In the commentary Dr Middleton discusses the implications of the difficulties I went through when communicating my relatives their genomic information.

Figure 1. Example of iAnn Announcement Service integrated in the British Society for Proteome Research Website.

iAnn increases access to announcements through its dissemination tools, which have been designed specifically to integrate posts across many different websites with minimal effort. iAnn allows reporting of events, courses or news to a central repository, which are then disseminated seamlessly to member scientific organizations or websites according to keywords, dates or geographical location. Forget about having to post your event or piece of news more than once for wide dissemination!

iAnn Community

Here is a list of organizations already benefiting from iAnn services. You can also be one of them:

• BSPR
• WILEY-VCH
• HUPO-PSI
• Bioinformatics Training Network
• ENFIN
• IMPPC
• ProteoRed

How can one join iAnn?

Currently there are several ways in which an organization may join iAnn. They can join as 1) Sponsor, 2) Member or 3) Collaborator. These categories are based on their needs and chosen commitment to the platform.

1. Sponsors usually have a priority for dissemination of the announcements and news. They are usually not involved in the curation process of announcements but contribute with funds to support iAnn’s centralized curation efforts.
2. Members are interested in both curation and wide dissemination of their own announcements. Typical members include iAnn widgets in their websites to offer the communities they serve permanently up-to-date relevant announcement information. For example, the British Society for Proteome Research (BSPR), depicted in Figue 1, shows a list of all the anouncements BSPR is interested in displaying in its website.
3. Collaborators are interested in posting announcements to the iAnn repository and helping us spread the word. In exchange we offer collaborators the ability to display iAnn announcements in their website for free.

Contact

Please contact us if you are interested. We look forward to hearing from you!

Unfortunately, people around the world are still trapped in the paper-based office paradigm when wanting to disseminate announcement information. Again and again they post their announcement to different places knowing that it will only reach a partial share of all potentially interested readers. They add data and clog online databases as no centralized repository is available for posting or getting information. Despite the great number of hours of work lost by millions of people trying to post, scientific organizations have been extremely slow to embrace community-shared announcement curation.

We (Rafael Jimenez and I) are promoting the creation of a community of organizations and people to lead iAnn, a centralized collaboration platform that coordinates curation efforts among scientific organizations. iAnn increases access to announcements through its dissemination tools, which have been designed specifically to integrate posts across many different websites with minimal effort. iAnn allows you to post your event, course, piece of news only once to a central repository, which is then disseminated seamlessly to relevant scientific organizations or websites according to keywords, dates or geographical location.

If you think iAnn is of interest to you please contact me (see contact information on the right) or wait for future developments that are about to come in Manuel Corpas’ Blog. Currently we are in a development phase for the project and would like to hear from potential users or scientific organizations if they have any thoughts or suggestions on the matter. Our aim is to change the way anyone posts and finds relevant information about any given professional field. iAnn promises to help many users keep up-to-date with relevant announcements more effortlessly. Perhaps from now on websites will be better able to have most of the events, courses, seminars, news, etc. that users would expect to find in them.

• AA: 6 (11.5%)
• AG or GA: 18 (34.6%)
• GG: 28 (53.8%)

If I was to speculate from this finding and assuming that the GG allele association is true, it would seem that being pro-social is quite dominant among Europeans. In fact when I look at the distribution of rs53576 alleles per populations in the 1000 genomes project, the above distribution looks quite similar to the proportions shown for the European (CEU) pie chart:

Frequencies of rs53576 in the 1000 genomes project. CEU: European; CHB+JPT: Han Chinese and Japanese; YRI: Yoruban (from Nigeria). More yellow apparently means more social.

Obviously the samples quite are small to make a final conclusion but I let readers judge by themselves what these results might mean.

I would like to thank Karyn Megy as she gave me the idea of querying the public domain 23andMe database.

To my pleasant surprise, all of my family are GG, except my aunt who is AG.

Family genotype for rs53576 SNP using myKaryoView. Clicking on graph features popups are released with type_id (genotype) information. Grouped popups include mine, sister, dad, mum. Independent, aunt.

In a post about the Kogan et al paper, Suzanne Elvidge writes that oxytocin, also known as the cuddle hormone, makes us feel good. It’s released during sexual intercourse, pair bonding and breastfeeding, and our levels (and the dog’s levels) rise when we stroke our pets. The oxytocin gene may also make us more optimistic. Differences in our responses to oxytocin seem to affect how empathic we are – so if you are a nice person, it might be (at least a little bit) down to your oxytocin gene.

Maybe my aunt’s temperament may not be just a consequence of her having red hair.

Tita, te quiero!

Beware of pasting gene names in an Excel spreadsheet with a default format, as these may be changed into dates.

From my current list of 19,026 genes that I have compiled as of now, here are the names of the genes that have been automatically changed by Excel into dates. In the table below, the first column denotes the date the gene name is changed to, the middle column the Ensembl ID of the gene and the right column the actual name that was changed by Excel into a date.

Sep-01    ENSG00000180096        SEPT1    
Sep-02    ENSG00000168385        SEPT2
Sep-03    ENSG00000100167        SEPT3
Sep-04    ENSG00000108387        SEPT4
Sep-05    ENSG00000184702        SEPT5
Sep-06    ENSG00000125354        SEPT6
Sep-07    ENSG00000122545        SEPT7
Sep-08    ENSG00000164402        SEPT8
Sep-09    ENSG00000184640        SEPT9
Sep-10    ENSG00000186522        SEPT10
Sep-11    ENSG00000138758        SEPT11
Sep-12    ENSG00000140623        SEPT12
Sep-14    ENSG00000154997        SEPT14

Mar-01    ENSG00000145416        MARCH1
Mar-02    ENSG00000099785        MARCH2
Mar-03    ENSG00000173926        MARCH3
Mar-04    ENSG00000144583        MARCH4
Mar-05    ENSG00000198060        MARCH5
Mar-06    ENSG00000145495        MARCH6
Mar-07    ENSG00000136536        MARCH7
Mar-08    ENSG00000165406        MARCH8
Mar-09    ENSG00000139266        MARCH9
Mar-10    ENSG00000173838        MARCH10
Mar-11    ENSG00000183654        MARCH11

Dec-01    ENSG00000173077        DEC1