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DNA Helix

Posts Tagged ‘deCODE’

Scientists use Iceland’s genealogical database to pinpoint the heritage of a deadly disease

A collaboration of scientists from Iceland and the United States has used Iceland’s genealogical database (by deCODE genetics) to trace the ancestors of patients suffering from hereditary cystatin C amyloid angiopathy (HCCAA). Analysis shows that the deadly mutation in the cystatin C gene, L68Q, derives from a common ancestor born roughly 18 generations ago, around 1550AD. Details are published June 20th in the open-access journal PLoS Genetics.

This dominantly inherited disease, which is due to a mutation in cystatin C (L68Q), strikes young adults with healthy blood pressure. The disease results in death from repeated brain haemorrhages, on average by the age of 30. The origin of the mutation causing HCCAA was previously unknown, but using DNA haplotype analysis the scientists have shed light on the history of this autosomal dominant disease that has high penetrance in contemporary Icelanders.

The scientists found that 200 years ago, obligate carriers of the mutation lived a normal life span compared to the control population (their spouses). In carriers born around 1820, however, a trend of shortening life span began, resulting in an average life span of only 30 years in people born around 1900. This 30-year lifespan has stayed constant since then in both men and women.

At the same time, a matrilinear effect appeared whereby those who inherited the mutation from the mother died earlier. For carriers born after 1900, the difference is a loss of 9.4 years for those who inherited the mutation from their mothers rather than their fathers. Based on this information, the authors propose that the traditional diet of the nation (which in the past consisted largely of whey-preserved offal as well as meat, dried fish, and butter) “protected” the mutation carriers for almost 300 years until the Icelandic diet changed early in the early 19th century, exemplified by drastic increases in imported carbohydrates and salt.

This finding has implications for studies of Alzheimer’s disease as cerebral amyloid angiopathy (CAA) is almost universally found in Alzheimer’s patients and normal cystatin C protein is one of the proteins found in amyloid in brains of Alzheimer’s patients. Studies are underway to try to elucidate the risk factors with the hope of providing a preventive stategy for cystatin L68Q carriers.

Source: Public Library of Science

Palsdottir A, Helgason A, Palsson S, Bjornsson HT, Bragason BT, et al. (2008) A Drastic Reduction in the Life Span of Cystatin C L68Q Carriers Due to Life-Style Changes during the Last Two Centuries. PLoS Genet 4(6): e1000099. doi:10.1371/journal.pgen.1000099

Josh says:

This is amazing. It almost makes me wish that the United States and other countries had a database like Iceland does, except I don’t really trust the US government. Regardless, as the costs for sequencing decrease, we should start to see more discoveries like this.

Fun: Icelandic DNA Runic Reading

Last week, I visited deCODE Genetics in Reykjavík, Iceland. To culturally prepare (procrastinate work), I hit my trusty Wikipedia to research all about Iceland.

Obviously, the first thing one needs to know when visiting Iceland is the ancient Viking runic system.

So, for a bit of Icelandic-cultural bio-blog genomics flare:

DNA Binary Rune Name Translation Unicode
AA 0000 (00) fe rune fe wealth 0×16A0
AG 0001 (01) ur rune ur rain 0×16A2
AC 0010 (02) thurs rune thurs giant
(as in Thursday)
0×16A6
AT 0011 (03) aesir rune as aesir 0×16AC
GA 0100 (04) reidh rune reidh journey 0×16B1
GG 0101 (05) kaun rune kaun ulcer 0×16B4
GC 0110 (06) hagall rune hagall hail 0×16BC
GT 0111 (07) naud rune naud need 0×16BE
CA 1000 (08) iss rune iss ice 0×16C1
CG 1001 (09) ar rune ar boon 0×16C5
CC 1010 (10) sol rune sol sun 0×16C8
CT 1011 (11) tyr rune tyr Tyr
(as in Tuesday)
0×16CF
TA 1100 (12) bjarken rune bjarken birch 0×16D2
TG 1101 (13) madhr rune madhr man 0×16D8
TC 1110 (14) logr rune logr waterfall 0×16DA
TT 1111 (15) yr rune yr yew 0×16E6

These runes and translations are from the Icelandic interpretation of the Younger Furthark runic system. (see runic font help below if rune characters appear as “?”) (runic letter pronunciation guide)

Two 2-bit (4 bases) bases together make a 4-bit number (16 runes). Nucleotide base numbering is based on this representation:

Base Purine[0]
Pyrimidine[1]
ID Base Number
adenine (A) 0 0 00 = 0
guanine (G) 0 1 01 = 1
cytosine (C) 1 0 10 = 2
thymine (T) 1 1 11 = 3
uracil (U) 1 -1 -11 = -3 OR
100 = -3

This representation is convenient because the Base Number both identifies the base as a Purine or Pyrimidine and can be inverted to get the base’s matching Base Number. (how are bases usually represented in bioinformatic software?)

~A = ~(00) = 11 = T or U
~G = ~(01) = 01 = C
~C = ~(10) = 10 = G
~T = ~(11) = 00 = A
~U = -(~(11)) = -00 = 00 = A

Font Support

To display Unicode Younger Futhark rune characters, you need a Unicode font supporting the Unicode runic range (pdf). I use Junicode (download font). To enter characters, the easiest way to enter non-standard Unicode characters on any system is to copy-and-paste from a text table (Wikipedia’s Unicode table of runic characters in plain-text).

FAQ

Q: Why not codons, the standard grouping of three nucleotides?

A: Because that would be 64 (4^3) symbols, and that’s too many to remember. However, if you don’t mind 64 new symbols, the Cirth runic language from “Lord of the Rings” has 64 runes (60 letters + 4 punctuation marks) —and it’s in LaTeX! (However, Cirth is not official unicode… yet) Using the same base-numbering scheme, one could make a DNA codon Runic map, too.

Q: Why Younger Furthark and not other Runic systems?

A: Because Younger Furthark just so happens to have exactly 16 characters.

Q: I have been to / am from Iceland and I have never needed to know this.

A: That’s not a question.

Q: Have you considered selling “Genetic Tests” by which you take an arbitrary DNA sequence, “translate” it into runes, and make it into some kind of trendy “runic fortune?” Considering that “alternative medicine” is some bazillion dollar industry and people already buy runic shit because it’s “cool” and “spiritual,” you’d probably make a killing… probably more than (technically) scientifically-legitimate genetic testing services.

A: What? What kind of asshole do you think I am? (It’s almost like I wrote my own FAQ questions or something.)

#RuneTable { border: none; margin: 1.6em auto; width: 90%; } #RuneTable tr { padding-bottom: 4px; border-bottom: 1px dotted #ccc; } #RuneTable th, #RuneTable td { vertical-align: top; text-align: left; margin-bottom: 0.6em; border-bottom: 1px dotted #ccc; } #RuneTable th {</p> <p>} td.RuneTable-binary, td.RuneTable-num, td.RuneTable-unicode { text-align: right !important; } #RuneTable td, #RuneTable th { padding: 2px 13px 2px 0px !important; } #BaseTable { border: none; margin: 1.6em auto; width: 70%; } #InverseTable { border: none; margin: 1.6em auto; width: 70%; } #BaseTable td, #BaseTable th, #InverseTable td, #InverseTable th { padding: 2px 13px 2px 0px !important; }