Harvard:Biophysics 101/Notebook:ZS/2007-3-15
From OpenWetWare
DONT LOOK AT ME
I'm supposed to be private :D a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
a
aa
a
a
a
a
a
BLAST Results
>ref|NT_030059.12|Hs10_30314 Homo sapiens chromosome 10 genomic contig, reference assembly
Length=44617998
Features flanking this part of subject sequence:
3895 bp at 5' side: hypothetical protein
425 bp at 3' side: HtrA serine peptidase 1
Score = 736 bits (398), Expect = 0.0
Identities = 400/401 (99%), Gaps = 0/401 (0%)
Strand=Plus/Plus
Query 1 CACCCTCGCCAGTTACGAGCTGCCGAGCCGCTTCCTAGGCTCTCTGCGAATACGGACACG 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 42968870 CACCCTCGCCAGTTACGAGCTGCCGAGCCGCTTCCTAGGCTCTCTGCGAATACGGACACG 42968929
Query 61 CATGCCACCCACAACAACTTTTTAAAAGAATCAGACGTGTGAAGGATTCTATTCGAATTA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 42968930 CATGCCACCCACAACAACTTTTTAAAAGAATCAGACGTGTGAAGGATTCTATTCGAATTA 42968989
Query 121 CTTCTGCTCTCTGCTTTTATCACTTCACTGTGGGTCTGGGCGCGGGCTTTCTGCCAGCTC 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 42968990 CTTCTGCTCTCTGCTTTTATCACTTCACTGTGGGTCTGGGCGCGGGCTTTCTGCCAGCTC 42969049
Query 181 CGCGGACGCTGCCTTCGTCCAGCCGCAGAGGCCCCGCGGTCAGGGTCCCGCGTGCGGGGT 240
|||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||
Sbjct 42969050 CGCGGACGCTGCCTTCGTCCGGCCGCAGAGGCCCCGCGGTCAGGGTCCCGCGTGCGGGGT 42969109
Query 241 ACCGGGGGCAGAACCAGCGCGTGACCGGGGTCCGCGGTGCCGCAACGCCCCGGGTCTGCG 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 42969110 ACCGGGGGCAGAACCAGCGCGTGACCGGGGTCCGCGGTGCCGCAACGCCCCGGGTCTGCG 42969169
Query 301 CAGAGGCCCCTGCAGTCCCTGCCCGGCCCAGTCCGAGCTTCCCGGGCGGGCCCCCAGTCC 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 42969170 CAGAGGCCCCTGCAGTCCCTGCCCGGCCCAGTCCGAGCTTCCCGGGCGGGCCCCCAGTCC 42969229
Query 361 GGCGATTTGCAGGAACTTTCCCCGGCGCTCCCACGCGAAGC 401
|||||||||||||||||||||||||||||||||||||||||
Sbjct 42969230 GGCGATTTGCAGGAACTTTCCCCGGCGCTCCCACGCGAAGC 42969270
OMIM Results
Looking under the HtrA serine pepidase 1 protein, through OMIM found: http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=602194&a=602194_AllelicVariant0001
Then, through NCBI SNP: http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs11200638 for the page, says:
>gnl|dbSNP|rs11200638|allelePos=201|totalLen=401|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=120 CACCCTCGCC AGTTACGAGC TGCCGAGCCG CTTCCTAGGC TCTCTGCGAA TACGGACACG CATGCCACCC ACAACAACTT TTTAAAAGAA TCAGACGTGT GAAGGATTCT ATTCGAATTA CTTCTGCTCT CTGCTTTTAT CACTTCACTG TGGGTCTGGG CGCGGGCTTT CTGCCAGCTC CGCGGACGCT GCCTTCGTCC R GCCGCAGAGG CCCCGCGGTC AGGGTCCCGC GTGCGGGGTA CCGGGGGCAG AACCAGCGCG TGACCGGGGT CCGCGGTGCC GCAACGCCCC GGGTCTGCGC AGAGGCCCCT GCAGTCCCTG CCCGGCCCAG TCCGAGCTTC CCGGGCGGGC CCCCAGTCCG GCGATTTGCA GGAACTTTCC CCGGCGCTCC CACGCGAAGC
Note that this matches exactly the SNP from the blast result.
Therefore, quoting OMIM:
MOLECULAR GENETICS From a cohort of Southeast Asians in Hong Kong, DeWan et al. (2006) identified 96 patients who had been previously diagnosed with wet age-related macular degeneration (see 610149) and 138 matched control individuals who were ARMD-free. Because the putative locus on 10q26 in which a previously identified SNP with significant association with ARMD had been removed from GenBank (see 610149), DeWan et al. (2006) sequenced the entire local genomic region, including promoters, exons, and intron-exon junctions of PLEKHA1 (607772) and HTRA1, in search of the functional variant. They found that 1 SNP in the promoter region of HTRA1, rs11200638(602194.0001), located 512 base pairs upstream of the HTRA1 putative transcriptional start site and 6,096 base pairs downstream of the previously identified SNP, exhibited a complete linkage disequilibrium pattern with the previously identified SNP. The SNP rs11200638 resides within putative binding sites for the transcription factors adaptor-related protein complex 2-alpha (AP2-alpha; 107580) and serum response factor (SRF; 600589). Preliminary results showed higher HRTA1 expression correlated with the risk (AA) compared with the wildtype (GG) genotype in in vitro transfection assays. Yang et al. (2006) independently identified the same SNP in the HTRA1 promoter region as causative of age-related macular degeneration in a Caucasian cohort in Utah. The authors suggested that the estimated population-attributable risk for the SNP is 49.3%. Consistent with an additive effect, the estimated population-attributable risk from a joint model with CFH Y402H (134370.0008) (i.e., for a risk allele at either locus) is 71.4%. ALLELIC VARIANTS (selected examples) .0001 MACULAR DEGENERATION, AGE-RELATED, 7 [HTRA1, -512G-A] MACULAR DEGENERATION, AGE-RELATED, NEOVASCULAR TYPE, SUSCEPTIBILITY TO, INCLUDED DeWan et al. (2006) identified a SNP (rs11200638) for which homozygosity for the AA genotype results in a 10-fold (confidence intervals 4.38 to 22.82) increased risk of wet age-related macular degeneration (see ARMD7, 610149) in a Southeast Asian population identified in Hong Kong. Yang et al. (2006) independently identified this variant as conferring risk in a Caucasian cohort from Utah.
Conclusion for this sequence
As a doctor, I would say that the patient may be at an increased risk for wet age-related macular degeneration, and that more tests are necessary to determine if he/she has a homozygous or heterozygous condition, which would affect the patient's risk factor. I would suggest possible preventative treatment for the disease, and suggest genetic screening with the husband to determine risk of passing trait.
What I did/would have done in Python
- Blast the sequence
- Search the protein of interest in OMIM and see if the BLAST matches any results
- 'Wouldnt this be hard to implement?'
- Put through written program to determine reading frame and AA mutation
- If intron, then probably not big deal
- If silent or same amino acid type, likewise
- If different AA type or causes frameshift/missense/nonsense mutation, then may be a big deal.
- Research revelant literature to make final conclusion
- 'Python can only tell you the literature to look at given sequence, if one is a good programmer...'
Zach's Mystery Sequence
>Bob's sequence - is he going to die? TACAAACATAACAAATCCATGTGGCTCTTCCACTGGAAAGACTTCAGGTAAAGAATCCAT AACCAGCCCCTGGTGGCTTGCGTGACAGTCTCCACACATCTCCAAAATTAACACTTTAGC TAAATTCTCTCCACATGGGATAGAATTGCTCTGCCACTGTCTGAAAATGCGTATGTATGT CTTCTTTCTTTGTGAGAAGTTTCTACATGAGATGCAGAAATTACCATCTCTACGGCTATT GGAAAATGTTGGCTCATTTTATAGCTGCTGGCATAGATTTTTCCAGAGATTTAAGTTTCA CTCCTCCGGTCATAATGAATCACATCTGTGTATTTGTACAACATTTCTCCCTTCTTCCAT TCACTGAAAGTATCCCTGCCTGTGAATGTGTAGGTTTA
Zach's Mystery Solution
DONT CLICK HERE IF YOURE SOLVING IT OR A PIG WILL LAND ON YOU AND SQUASH YOU ALIVE. click here
