Wednesday, February 22, 2012

OPRM1-mu Opioid receptor


Your data includes 127 SNPs on gene OPRM1, which is on chromosome 6.
MAF Source: 1000 Genomes
http://www.1000genomes.org/
TUESDAY FEBRUARY 14, 2012
February 2012 Updated Genotypes for Integrated Phase 1 Release


This February 2012  release represents a new improved set of phased genotypes for our integrated phase 1 variant release. This release contains SNPS, short INDELs and Deletions based on low coverage and exome sequencing data across 1092 individuals.


Please note the sites list has been filtered to remove a small number of indels which were discovered to have a high false positve rate. There is more information about this in the README 
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/README.phase1_integrated_release_version2_20120214
==================================================

OPRM1 154402201 rs6912029 G or T GG
MAF/MinorAlleleCount: T=0.061/133
OPRM1 154402389 rs1799972 C or T CC
MAF/MinorAlleleCount: T=0.068/149
OPRM1 154402490 rs1799971 A or G AG
MAF/MinorAlleleCount: G=0.189/414
OPRM1 154409860 rs514980 C or T TT
MAF/MinorAlleleCount: C=0.154/338
OPRM1 154410479 rs509544 C or T TT
MAF/MinorAlleleCount: C=0.156/341
OPRM1 154410691 rs4870266 A or G GG
MAF/MinorAlleleCount: A=0.093/203
OPRM1 154414130 rs607759 C or T CC
MAF/MinorAlleleCount: T=0.156/341
OPRM1 154414385 rs499796 A or G AA
MAF/MinorAlleleCount: G=0.238/521
OPRM1 154419618 rs3778146 C or T TT
MAF/MinorAlleleCount: C=0.113/248
OPRM1 154420845 rs3823010 A or G GG
MAF/MinorAlleleCount: A=0.112/244
OPRM1 154425351 rs3778150 C or T TT
MAF/MinorAlleleCount: C=0.132/288
OPRM1 154429999 rs6927269 G or T TT
MAF/MinorAlleleCount: G=0.108/236
OPRM1 154431672 rs4357147 A or G AA
MAF/MinorAlleleCount: G=0.018/40
OPRM1 154433062 rs1461773 A or G GG
dbSNP Orientation: Minus
dbSNP Genotype: CC
MAF/MinorAlleleCount: A=0.116/253
OPRM1 154433828 rs6923231 A or G GG
MAF/MinorAlleleCount: A=0.070/153
OPRM1 154434831 rs589046 C or T CC
MAF/MinorAlleleCount: T=0.305/668
OPRM1 154435373 rs3778151 C or T TT
MAF/MinorAlleleCount: C=0.166/364
OPRM1 154435577 rs3778153 A or C CC
MAF/MinorAlleleCount: A=0.110/240
OPRM1 154449660 rs563649 C or T CC
MAF/MinorAlleleCount: T=0.104/228
OPRM1 154451807 rs9479756 A or G GG
MAF/MinorAlleleCount: A=0.097/212
OPRM1 154452803 rs17174794 C or G CC
MAF/MinorAlleleCount: G=0.003/7
OPRM1 154452817 rs17174801 A or G AA
MAF/MinorAlleleCount: G=0.003/7
OPRM1 154454948 rs10485057 A or G AA
MAF/MinorAlleleCount: G=0.100/218
OPRM1 154455121 rs510587 A or G GG
MAF/MinorAlleleCount: A=0.032/71
OPRM1 154456068 rs9282821 A or C AC
MAF/MinorAlleleCount: A=0.401/877
OPRM1 154456139 rs540825 A or T AT
dbSNP Orientation: Minus
dbSNP Genotype: AT
MAF/MinorAlleleCount: A=0.127/277
OPRM1 154456256 rs675026 A or G AG
dbSNP Orientation: Minus
dbSNP Genotype: CT
MAF/MinorAlleleCount: A=0.241/528
OPRM1 154456266 rs562859 C or T CT
dbSNP Orientation: Minus
dbSNP Genotype: AG
MAF/MinorAlleleCount: C=0.277/605
OPRM1 154457127 rs660756 G or T GT
MAF/MinorAlleleCount: G=0.276/603
OPRM1 154459438 rs12203621 A or G GG
MAF/MinorAlleleCount: A=0.064/139
OPRM1 154459840 rs548646 C or T CT
MAF/MinorAlleleCount: T=0.296/648
OPRM1 154460107 rs3798683 A or G GG
MAF/MinorAlleleCount: A=0.192/421
OPRM1 154461748 rs679987 C or T TT
MAF/MinorAlleleCount: C=0.067/147
OPRM1 154463422 rs1323043 C or T CT
MAF/MinorAlleleCount: T=0.136/297
OPRM1 154464437 rs647192 A or G AG
MAF/MinorAlleleCount: G=0.136/297
OPRM1 154466013 rs9322447 A or G AG
MAF/MinorAlleleCount: A=0.441/966
OPRM1 154466180 rs619089 A or G AG
dbSNP Orientation: Minus
dbSNP Genotype: CT
MAF/MinorAlleleCount: G=0.296/647
OPRM1 154470229 rs650825 A or G AG
dbSNP Orientation: Minus
dbSNP Genotype: CT
MAF/MinorAlleleCount: A=0.166/364
OPRM1 154470394 rs650245 A or G GG
MAF/MinorAlleleCount: A=0.115/251
OPRM1 154477398 rs9478506 G or T GG
MAF/MinorAlleleCount: T=0.088/193
OPRM1 154477679 rs606148 A or C CC
MAF/MinorAlleleCount: A=0.072/157
OPRM1 154478944 rs632395 A or G GG
MAF/MinorAlleleCount: A=0.101/220
OPRM1 154482434 rs671531 A or G AG
MAF/MinorAlleleCount: A=0.279/610
OPRM1 154483556 rs558948 C or T CT
MAF/MinorAlleleCount: T=0.163/357
OPRM1 154483822 rs645027 A or G AA
dbSNP Orientation: Minus
dbSNP Genotype: GG
MAF/MinorAlleleCount: G=0.129/283
OPRM1 154484971 rs613341 C or T CC
MAF/MinorAlleleCount: T=0.072/157
OPRM1 154486907 rs10485058 A or G AA
MAF/MinorAlleleCount: G=0.099/217
OPRM1 154491542 rs613355 A or C AC
MAF/MinorAlleleCount: C=0.272/595
OPRM1 154493504 rs649840 A or C CC
MAF/MinorAlleleCount: A=0.147/321
OPRM1 154494178 rs636433 A or G GG
dbSNP Orientation: Minus
dbSNP Genotype: CC
MAF/MinorAlleleCount: A=0.076/166
OPRM1 154496957 rs7774038 C or T TT
MAF/MinorAlleleCount: C=0.051/111
OPRM1 154497880 rs686633 C or T CT
MAF/MinorAlleleCount: T=0.128/281
OPRM1 154499185 rs544093 G or T TT
MAF/MinorAlleleCount: G=0.086/189
OPRM1 154499899 rs2010884 A or G GG
MAF/MinorAlleleCount: A=0.225/493
OPRM1 154500548 rs655059 C or T TT
MAF/MinorAlleleCount: C=0.056/122
OPRM1 154502815 rs13203628 A or G AG
MAF/MinorAlleleCount: G=0.216/472
OPRM1 154502966 rs12660296 C or T CT
MAF/MinorAlleleCount: C=0.216/472
OPRM1 154503514 rs13193545 C or T TT
MAF/MinorAlleleCount: C=0.098/215
OPRM1 154503778 rs9397687 C or T CT
MAF/MinorAlleleCount: T=0.416/910
OPRM1 154504070 rs518596 A or G GG
dbSNP Orientation: Minus
dbSNP Genotype: CC
MAF/MinorAlleleCount: G=0.366/800
OPRM1 154504084 rs10223804 A or G GG
MAF/MinorAlleleCount: A=0.079/173
OPRM1 154504746 rs6557337 C or T CT
MAF/MinorAlleleCount: T=0.426/931
OPRM1 154506022 rs569284 A or C AA
dbSNP Orientation: Minus
dbSNP Genotype: TT
MAF/MinorAlleleCount: C=0.086/188
OPRM1 154506891 rs12207811 C or T CC
MAF/MinorAlleleCount: T=0.157/344
OPRM1 154508510 rs4869817 A or G AG
MAF/MinorAlleleCount: G=0.455/995
OPRM1 154511909 rs9397178 A or G AA
MAF/MinorAlleleCount: G=0.162/354
OPRM1 154512887 rs13196610 A or G AA
MAF/MinorAlleleCount: G=0.046/100
OPRM1 154514019 rs4870268 C or T TT
MAF/MinorAlleleCount: C=0.405/887
OPRM1 154516563 rs9383693 C or T CC
MAF/MinorAlleleCount: C=0.467/1022
=====================================================
Interaction Protein for Cytohesin Exchange Factors 1 
(IPCEF1) Binds Cytohesin 2 and Modifies Its Activity
http://www.jbc.org/content/278/44/43460.full
=====================================================

OPRM1 154517641 rs17085103 G or T TT
MAF/MinorAlleleCount: G=0.061/134

OPRM1 154518220 rs9479767 C or T TT
MAF/MinorAlleleCount: T=0.470/1029
OPRM1 154519605 rs17277929 C or T TT
MAF/MinorAlleleCount: C=0.098/215
OPRM1 154520132 rs2236256 A or C CC
MAF/MinorAlleleCount: C=0.471/1030
OPRM1 154520428 rs6916787 A or G GG
MAF/MinorAlleleCount: A=0.061/133
OPRM1 154523086 rs1950005 A or G GG
MAF/MinorAlleleCount: G=0.476/1042
OPRM1 154523859 rs1918760 C or T CC
MAF/MinorAlleleCount: C=0.265/579
OPRM1 154523921 rs1918761 C or T TT
dbSNP Orientation: Minus
dbSNP Genotype: AA
MAF/MinorAlleleCount: T=0.265/579
OPRM1 154524838 rs9479769 G or T TT
MAF/MinorAlleleCount: G=0.387/846
OPRM1 154527332 rs12199124 A or G GG
MAF/MinorAlleleCount: A=0.164/358
OPRM1 154529113 rs2281617 C or T CC
MAF/MinorAlleleCount: T=0.238/520
OPRM1 154529487 rs6939625 A or G GG
MAF/MinorAlleleCount: A=0.090/198
OPRM1 154529669 rs6941251 C or T CC
MAF/MinorAlleleCount: C=0.353/773
OPRM1 154532350 rs6938037 A or C AA
MAF/MinorAlleleCount: A=0.246/538
OPRM1 154532829 rs12208947 A or G no call
MAF/MinorAlleleCount: A=0.216/473
OPRM1 154534546 rs7745499 A or C AA
MAF/MinorAlleleCount: A=0.350/765
OPRM1 154541831 rs13437608 C or T C
MAF/MinorAlleleCount: T=0.056/122
OPRM1 154542817 rs17278409 C or T CC
MAF/MinorAlleleCount: T=0.177/387
OPRM1 154543825 rs9479778 C or T TT
MAF/MinorAlleleCount: C=0.012/27
OPRM1 154544380 rs9479779 A or G AA
MAF/MinorAlleleCount: G=0.049/108
OPRM1 154545204 rs11965988 C or T TT
MAF/MinorAlleleCount: C=0.076/166
OPRM1 154545564 rs9371331 A or G AA
MAF/MinorAlleleCount: G=0.202/441
OPRM1 154545712 rs9479780 C or T TT
MAF/MinorAlleleCount: T=0.346/756
OPRM1 154554189 rs7452342 C or T TT
MAF/MinorAlleleCount: T=0.266/583
OPRM1 154554890 rs4626436 A or G GG
MAF/MinorAlleleCount: A=0.080/175
OPRM1 154557793 rs10485060 A or C CC
MAF/MinorAlleleCount: A=0.087/191
OPRM1 154558954 rs11970612 A or C AA
MAF/MinorAlleleCount: C=0.081/178
OPRM1 154560330 rs1040822 G or T TT
MAF/MinorAlleleCount: G=0.331/725
OPRM1 154562084 rs2295676 A or G AA
MAF/MinorAlleleCount: A=0.230/503
OPRM1 154564353 rs9322451 A or G GG
MAF/MinorAlleleCount: A=0.324/708+
OPRM1 154564432 rs1852629 C or T TT
MAF/MinorAlleleCount: T=0.340/745
OPRM1 154569846 rs6557339 C or T CC
MAF/MinorAlleleCount: C=0.245/536
OPRM1 154571206 rs9479791 C or T CC
MAF/MinorAlleleCount: T=0.182/399
OPRM1 154572672 rs6913456 A or G GG
MAF/MinorAlleleCount: G=0.417/912
OPRM1 154576104 rs790252 A or G AA
MAF/MinorAlleleCount: A=0.183/400
OPRM1 154576968 rs9478525 A or G GG
MAF/MinorAlleleCount: A=0.060/132
OPRM1 154577270 rs9478526 A or C AA
MAF/MinorAlleleCount: C=0.064/141
OPRM1 154581998 rs790262 A or G GG
MAF/MinorAlleleCount: G=0.486/1063
OPRM1 154584183 rs2272381 A or G AA
MAF/MinorAlleleCount: G=0.186/408
OPRM1 154585010 rs12205120 G or T GG
MAF/MinorAlleleCount: T=0.146/319
OPRM1 154590121 rs2103277 G or T GG
MAF/MinorAlleleCount: G=0.266/581
OPRM1 154592545 rs9397697 A or G AA
MAF/MinorAlleleCount: A=0.179/392
OPRM1 154592810 rs12212773 A or G AA
MAF/MinorAlleleCount: G=0.153/335
OPRM1 154593899 rs9371781 A or C CC
MAF/MinorAlleleCount: C=0.278/609
OPRM1 154596299 rs17292684 A or C AA
MAF/MinorAlleleCount: C=0.033/72
OPRM1 154602029 rs6935927 C or T CC
MAF/MinorAlleleCount: C=0.345/755
OPRM1 154605345 rs9479796 G or T TT
MAF/MinorAlleleCount: G=0.381/834
OPRM1 154607027 rs4314511 A or G AA
MAF/MinorAlleleCount: G=0.261/570
OPRM1 154608434 rs11155954 G or T GG
MAF/MinorAlleleCount: T=0.175/382
OPRM1 154608539 rs7754313 G or T GG
MAF/MinorAlleleCount: T=0.020/43
OPRM1 154609076 rs9383697 C or T CC
MAF/MinorAlleleCount: C=0.227/497
OPRM1 154609368 rs7759388 A or G GG
MAF/MinorAlleleCount: A=0.099/216

Friday, February 3, 2012

Censored By 23andMe




MEDICAL FACTS:
My gallbladder died-emergency removal
Gallstones-My risk=11.1%=1.58x7.0%Typ.

Hypertriglyceridemia [started decade ago], yet my data says I have typical odds:
rs964184-CC

Diagnosed as bipolar for almost two decades and meds made my high stress career liveable, 
but my data says I have reduced odds:
rs4948418- CC

True Believers think:
1.Large segment sizes are passed intact and are proof we have detectable cousins. 
2.Segments are tested and can be detected in 23andMe raw data. 
3.They are doing a public service when they stalk others to proselytize and/or intimidate 
them with harassment. 
4.I care about their opinions even when Iam mostly revolted by them. manipulative and 
abusive stalking of me on every post, including those where I originated the topic. 
5.Consider it their duty to derail the posts and topics of with whom they disagree with 
personal attacks and irrelevant off topic provocations.

Invisible Pink Unicorn in its Natural Habitat
http://www.facebook.com/photo.php?fbid=10150538693581457

With the Hopes that our World is built on they were utterly out of touch,
They denied that the Moon was Stilton; they denied she was even Dutch;
They denied that Wishes were Horses; they denied that a Pig had Wings;
So we worshipped the Gods of the Market Who promised these beautiful things.
Rudyard Kipling-The Gods of the Copybook Headings

Do not try to convince the True Believers.
This is my list to remind myself not to respond to their provoking remarks:
thetick:
fauxdk:
AndreaBadger:
GeeBee of Bavaria:
Geneadict:
altai volk:
Maureen Higgins Markov:
Tanaquil:
Glenn N.:
MMaddi:
DNFTT

Family Surnames
Beauchamp, Bird, Blythe, Carruthers, Childress, Ehart, Fielding, Gowder, Hall, Headen, 
Hobson, Hueston, Little, Massey, McConnell, McDonald, Montgomery, Moore, Norwood, 
Reinholds, Reynolds, Rucker, Scharf, Shurvington, Woods, Work

Family Locations
Oregon, Washington, Kentucky, Arkansas, Texas, Georgia, South Carolina, North Carolina, 
Virginia, Scotland, Kent, England, Ireland, Germany, France, Ireland, Isle of Sky,

Family Locations
Geographic Facts: 
Father-orphaned in Denver;lived in Nebraska. Mother born Arkansas;ancestry in KY, GA, SC, 
NC,&Virginia. 

My maternal lineage is, starting with my mother:
Noda Moore-AR
Lillian Rucker-AR
Susan Willie Caldoni Saffroni Little-AR
Susan Childress-AR
Susan Elvina Childress-GA
Sarah Massey-NC
Sarah Work-SC
Margaret [Unknown]-VA
This is a reader's digest version of my maternal lineage:
http://webspace.webring.com/people/tu/um_910/MOORE.HT

About My Family
Diagnosed Type II Diabetes though my data say I have average risk:
rs7903146-CT
Type 2 Diabetes:My Risk=25.3%=.98x25.7% Typical risk
I have T2D/Type II Diabetes and one maternal aunt who has it. It did not start until my 
mid-50s. I retired from 26 years of working in corrections, which kept me physically 
active. 

I have hypertriglerides and we have yet to get them under control, which may be why my 
mother/aunts were affected with late onset AD.  Diet does not seem to work. Meds do not 
seem to work. I may have to exercise more. 

All my med. history is documented with my health insurance company and my offspring are 
few, so I am willing to participate in any research. My full genome sequence for my mtDNA 
is already public with the NCIB and I am an open book on my medical history.

I am diagnosed and treated for being bipolar. The True Believers who have not yet 
admitted and gotten treatment are a pain.

MY DNA MADE PUBLIC:
http://www.law.cornell.edu/uscode/usc_sec_42_00001320---d006-.html
http://www.fbi.gov/atlanta/press-releases/2011/fake-doctor-sentenced-for-health-care-
fraud-and-criminal-hipaa-violations

I am J1c3d yDNA and H3 mtDNA per FTDNA
These are my places for data on my DNA:

Haplogroup J1c3d
P58+ M267+ L147.1+ M369- M368- M367- L65.2- L222.2- L174-

Haplogroup - H3
HVR1 differences from CRS:16519C 
HVR2 differences from CRS:263G,315.1C 
CR differences from CRS:750G,1438G,4769G,6776C,714­8C, 8860G,15326G,15519C

My mtDNA Fasta File

My mtDNA Data Processed
http://testing-johnlloydscharf.blogspot.com/2011/12/my-ydna.html

X STRS:

Autosomal STRS: 

Notes On My 23andMe Raw Data

My mtDNA haplogroup/haplotype: 

My mtDNA disease profile: 

My yDNA haplotype 

My yDNA haplogroup 

My yDNA STRs 

My autosomal STRs 

My X-STRs 


23andMe kit number:
GED M211533
GED M083415
GED Kit Number: F125649
FTDNA Kit Number: 125649A
My raw data at:
Process it at one of the following. 

Database for Autism:

List of SNP-trait associations

For those who believe "Race" is a scientific concept:

On FTDNA, my shared cM runs from 20.77cM to 66.02cM and includes 138 individuals.
23andM for the same range of 20.77cm to 66.02cM in RF, it includes 41 individuals.



About Me
Tiffany at 23andMe Customer Service (Tiffany B.) wrote:Dec 20, 2011
(6 hours ago)
John,

We have suspended your Community posting privileges effective immediately. Your recent posts are in violation of the Terms of Service agreement as well as our Community Guidelines. See https://www.23andme.com/about/tos/and https://www.23andme.com/you/community/guidelines/ 

Please note that you still have the ability to send and receive messages and invitations. Also, this revocation does not affect access to your data or account. Should we receive reports from other users that you are abusing the messaging system, that privilege will also be terminated immediately without notice.

Let me know if you have any questions.

Sincerely,
Tiffany



http://www.facebook.com/note.php?note_id=10150437853467727

Wednesday, August 25, 2010

DNA Infallibility

New Scientist has an article making the case that DNA testing is neither clear-cut nor definitive:


... much of the DNA analysis now conducted in crime labs can suffer from worrying subjectivity and bias. We asked forensic analysts to interpret a sample of real DNA evidence and found that they reached opposing conclusions about whether the suspect matched it or not. Our subsequent survey of labs around the world also shows that there are significant inconsistencies in the guidelines on how to interpret a sample. The findings suggest that the difference between prison and freedom could often rest on the opinions of a single individual.

. . .

We took a mixed sample of DNA evidence from an actual crime scene- a gang rape committed in Georgia, US- which helped to convict a man called Kerry Robinson, who is currently in prison. We presented it, and Robinson's DNA profile, to 17 experienced analysts working in the same accredited government lab in the US, without any contextual information that might bias their judgement.

In the original case, two analysts from the Georgia Bureau of Investigation concluded that Robinson "could not be excluded" from the crime scene sample, based on his DNA profile. (A second man convicted of the same crime also testified that Robinson was an assailant, in return for a lesser jail term.) Each of our 17 analysts independently examined the profiles from the DNA mixture, the victim's profile and those of two other suspects and was asked to judge whether the suspects' profiles could be "excluded", "cannot be excluded" or whether the results were "inconclusive".

If DNA analysis were totally objective, then all 17 analysts should reach the same conclusion. However, we found that just one agreed with the original judgement that Robinson "cannot be excluded". Four analysts said the evidence was inconclusive and 12 said he could be excluded.

"Fingerprinting and other forensic disciplines have now accepted that subjectivity and context may affect their judgement and decisions," says Dror. "It is now time that DNA analysts accept that under certain conditions, subjectivity and even bias may affect their work." Dror presented the results at the Green Mountain DNA conference in Burlington, Vermont, last month.

Christine Funk, an attorney in the Office of the Public Defender for the State of Minnesota, says the results of New Scientist's survey have profound implications for criminal justice. "The difference between prison and freedom rests in the hands of the scientist assigned the case," she says.

. . .

So what can be done? This year, the Scientific Working Group on DNA Analysis Methods (SWGDAM), which issues guidance to US labs performing forensic DNA analysis, published new recommendations regarding the interpretation of forensic DNA.

. . .

It seems lab managers would welcome consistent rules. Forensic lab directors at the 19 labs we surveyed also provided their views about how their analysis is currently done: 15 either agreed or strongly agreed that interpretation procedures should be based on national standards, and 11 agreed or strongly agreed that decisions over alleles should not be based on analyst opinion.

Labs must also take steps to avoid bias. Butler says that some labs continue to insist upon seeing suspect profiles before analysing evidence from the crime scene, which could lead to biased decision-making (see "Crime Scene Investigation: Impartiality"). Analysts also often know too much about a suspect and other evidence to be impartial, and public labs often have close ties to police. "Crime labs, including DNA labs, should not be under the control of a law enforcement agency," says one US analyst, who wished to remain anonymous. "We are scientists, not cops or prosecutors."

Wednesday, March 3, 2010

Monday, January 11, 2010

The Right to Confront Witnesses

http://www.nytimes.com/2010/01/11/opinion/11mon2.html

"Just last June, the Supreme Court decided that when prosecutors rely on lab reports they must call the experts who prepared them to testify. It was an important ruling, based on a defendant’s right to be confronted with witnesses against him, but the court is about to revisit it. The justices should reaffirm that the Sixth Amendment requires prosecutors to call the lab analysts whose work they rely on."