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I have to commend the father for such a valiant effort. However, shouldn't he have been able to automate part of the process, if he was manually comparing prin

by kqr2 18y ago

I have to commend the father for such a valiant effort. However, shouldn't he have been able to automate part of the process, if he was manually comparing printouts to the Ensembl reference genome? The job was daunting: The printouts contained data for approximately 20,000 base pairs, and there was no feasible way to automate the hunt for variants. After putting in a full day of consulting and then getting the kids to bed, Rienhoff would retire to his attic and spend hours checking Beatrice's adenines (A), thymines (T), guanines (G), and cytosines (C) against the Ensembl reference genome.

Eliezer 18y ago
Yeah, that struck me as odd too. This is supposed to be an automated job from what I heard.
a-priori 18y ago
Who knows the real story. This could be a case of the author taking journalistic liberties, or simply misunderstanding the process. My understanding is that a simple diff would take care of 90% of the work by eliminating all common base pairs. Then, from the results, his job would be to cross-reference each of the mutations against the gene database. Any unknown mutation could be the one he's looking for. Perhaps this is actually what he did, and the "no feasible way to automate the hunt" refers to the cross-referencing step, not the differencing step. Still though, reading that part almost made me email him saying, "I'll find you a way to automate it!".
- a-priori 18y ago
  So I just emailed Dr. Rienhoff, linking to this page, and encouraging him to post any problems he encounters to HN.
- etal 18y ago
  Here's his own telling of the story: http://mydaughtersdna.org/Members/hyrjr/the-reasoning-behind-the-dna-analysis http://mydaughtersdna.org/Members/hyrjr/the-reasoning-behind... An example of the zigzag pattern he probably received from the sequencing lab (his would have been much larger): http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000135503;r=12:50631753-50677124;t=ENST00000257963 http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=co... The reference sequence for the gene (this is what he was looking at): http://www.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000135503;r=12:50631753-50677124;t=ENST00000257963 http://www.ensembl.org/Homo_sapiens/Transcript/Exons?db=core... and his manual diff (at his site): http://mydaughtersdna.org/Members/hyrjr/acvr1b http://mydaughtersdna.org/Members/hyrjr/acvr1b The usual way to do a gene diff is by aligning two sequences with a program like ClustalW (free, and packaged with Debian now). That shows the differences and positions in a format other programs can read. But I don't know how much annotation the lab gave him, and annotating a pile of introns and exons does take a long time, even with the right tools -- the diffs aren't necessarily helpful until the rest of that information is in place.
kqr2 18y ago
Ensembl has a perl module / api for accessing their database: http://www.ensembl.org/info/docs/api/index.html http://www.ensembl.org/info/docs/api/index.html

by kqr2 18y ago

Eliezer 18y ago

Yeah, that struck me as odd too. This is supposed to be an automated job from what I heard.

a-priori 18y ago

Who knows the real story. This could be a case of the author taking journalistic liberties, or simply misunderstanding the process. My understanding is that a simple diff would take care of 90% of the work by eliminating all common base pairs. Then, from the results, his job would be to cross-reference each of the mutations against the gene database. Any unknown mutation could be the one he's looking for. Perhaps this is actually what he did, and the "no feasible way to automate the hunt" refers to the cross-referencing step, not the differencing step. Still though, reading that part almost made me email him saying, "I'll find you a way to automate it!".

a-priori 18y ago
So I just emailed Dr. Rienhoff, linking to this page, and encouraging him to post any problems he encounters to HN.
etal 18y ago
Here's his own telling of the story: http://mydaughtersdna.org/Members/hyrjr/the-reasoning-behind-the-dna-analysis http://mydaughtersdna.org/Members/hyrjr/the-reasoning-behind... An example of the zigzag pattern he probably received from the sequencing lab (his would have been much larger): http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000135503;r=12:50631753-50677124;t=ENST00000257963 http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=co... The reference sequence for the gene (this is what he was looking at): http://www.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000135503;r=12:50631753-50677124;t=ENST00000257963 http://www.ensembl.org/Homo_sapiens/Transcript/Exons?db=core... and his manual diff (at his site): http://mydaughtersdna.org/Members/hyrjr/acvr1b http://mydaughtersdna.org/Members/hyrjr/acvr1b The usual way to do a gene diff is by aligning two sequences with a program like ClustalW (free, and packaged with Debian now). That shows the differences and positions in a format other programs can read. But I don't know how much annotation the lab gave him, and annotating a pile of introns and exons does take a long time, even with the right tools -- the diffs aren't necessarily helpful until the rest of that information is in place.

kqr2 18y ago

Ensembl has a perl module / api for accessing their database: http://www.ensembl.org/info/docs/api/index.html http://www.ensembl.org/info/docs/api/index.html