User:JohnLloydScharf

Graduate [BS]of School of Community Services and Public Affairs with 242 credit hours and course work in research in sociology, psychology, and math at 400 level [Senior].... John Lloyd Scharf 23:02, 28 August 2011 (UTC)

Tested with New FTDNA-Family Finder Change in Platforms And Ordered 23andMe:[edit]

FTDNA[edit]

"On February 1st, 2011, Family Tree DNA changed testing platforms for our Family Finder autosomal DNA test. "We changed to the Illumina Omni platform. As part of that change, we retested for FREE all Family Tree DNA customers who previously ordered and paid for a Family Finder test. The new microarray chip for our Family Finder test is the Illumina OmniExpress. It tests about 710,000 unique autosomal DNA SNPs (single nucleotide polymorphisms). "The Omni platform provides better long-term upgrade options than the Affymetrix platform."

http://www.familytreedna.com/faq/answers.aspx?id=39

Useful Sites[edit]

http://genome.ucsc.edu/index.html

Faulty SNPedia Designations[edit]

Note that SNPedia claim of a SNP being tested, "FTDNA2" or "FTDNA" do not necessarily mean it was tested by FTDNA- EXAMPES

rs11276 12 14884706 CC- http://www.snpedia.com/index.php/Rs11276 - is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
Rs11391-http://www.snpedia.com/index.php/Rs11391 was tested on neither chip used by FTDNA.
rs11701 14 20231893 TG- http://www.snpedia.com/index.php/Rs11701 - is the older FTDNA Affy test, but this was not tested with the Illumina test chip.
"rs1205","1","157948857","TT" - http://www.snpedia.com/index.php/Rs1205 is the newer Illumina test, but this was not tested with the Affy test chip.
rs1835740 8 98236089 CC-http://www.snpedia.com/index.php/Rs1835740 - is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
Rs11718863 Not tested by FTDNA.
Rs1024161 Not tested by FTDNA.
rs1061170 1 194925860 TT - is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
rs1473473 12 70690645 TT - is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
rs1487275 12 70696559 AA - is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
rs1532701 16 54255528 AG - is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
rs36029 16 54254257 AG - is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
rs1566652 16 54289076 TT - is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
rs5743810 4 38506745 AG - is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
"rs2232596","20","36422795","AG" & rs2232596 20 36422795 AG Tested by FTDNA on old and new chips.
Rs7900744-Not tested by FTDNA.
rs4986764 17 57118129 GG-is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
rs1861046 4 15007004 GG-is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
rs11892031 2 234230022 AA-is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
rs7586110 2 234255266 TT-is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.
rs2232165 3 173648838 GG-is on the older FTDNA Affy test, but this was not tested with the Illumina test chip.

Contradictory Results[edit]

"rs11574","1","23758085","CC" from "FTDNA2" or Illumina versus rs11574 1 23758085 TC from "FTDNA" or Affy.

23andMe Ordered On 09/29/2011[edit]

I had a bunch SNPs I needed, starting with the triglycerides.

Ordered 09/29/11

Received 10/05/11

Collected 10/06/11

Mailed on 10/06/11

Received 10/20/11

Since they claim it will take six to eight weeks, then I should have results no later than 12/15/11 for a total of eleven weeks.

Time will tell. Since I ordered and paid for it online on 09/29/11, it has already been three weeks. When FTDNA processed me, ordered 06/29/08 and received yDNA Results on 09/05/09 and mtDNA Results on 09/11/09 or under eight weeks. I ordered my Family Finder SNPs test on 08/02/10 and received the results on 10/11/10, or ten weeks.

They posted the results on 11/06/11

FTDNA and 23andMe[edit]

FTDNA and 23andMe comparison

Editing Orientation[edit]

If the value is 'plus' you don't need to do anything, 23andMe agrees with dbSNP.
If the value is "minus" you need to change:

A->T
T->A
C->G
G->C

MY Personal SNP Results:[edit]

Disease Risks[edit]

Gallbladder Disease[edit]

"rs3758650","11","606865","GG"

The research indicated gallstone disease was negligible for the group researched. My gallbladder died and I do not know the cause.

Lactose Intolerance[edit]

Rs4988235Orientation minus

"rs4988235","2","136325116","AA"=TT

rs4988235Orientation minus

rs4988235 2 136325116 AA=TT

rs182549

"rs182549","2","136333224","TT"

I have not been diagnosed as lactose intolerant, but I show many symptoms of it.

http://en.wikipedia.org/wiki/Lactose_intolerance

Longevity[edit]

Researchers at Harvard Medical School and UC Davis have discovered a few genes that extend lifespan, suggesting that the whole family of SIR2 genes is involved in controlling lifespan. The findings are reported July 28, 2005 in the advance online edition of Science.

What We [FTDNA] Test: We test the rs1042522(C;G), rs1800795(G;G), rs2802292(A;A), rs2811712(A;A), rs34516635(G;G), rs3758391(C;C), and rs5882(A;G) SNPs.

Medications[edit]

Medications Page

New SNPs[edit]

"rs37973","7","7974401","AA"

FTDNA Illumina; Not FTDNA Affy

Normal/Most Common

http://www.snpedia.com/index.php/Rs37973

Nicotine Dependence[edit]

rs1435252 9 100143412 GG=AA Orientation minus
Rs3780422 NONE
"rs2779562","9","100317502","CC"
"rs3750344","9","100380137","TT"=AA Orientation minus
"rs2491397","9","100244983","TC"
"rs2184026","9","100344169","--"

http://www.snpedia.com/index.php/Rs3750344

[PMID 15759211] Associated with Nicotine Dependence as part of several haplotypes, based on a study of 1,000+ subjects including both African-Americans and European-Americans. Interestingly, the risk allele varies between populations. Among African-Americans, the haplotype C-C-G of rs2491397-rs2184026-rs3750344 [TC-(--)-AA] had a significant positive association with nicotine dependence. Among European-Americans, for rs1435252-rs3780422-rs2779562-rs3750344, the C-A-C-A haplotype[AA-NN-CC-AA] was positively associated with nicotine dependence while the T-A-T-A haplotype was negatively associated.[PMID 15759211]

"rs16969968","15","76669980","AG"

rs16969968 increases susceptibility to Substance dependence, Nicotine 1.10 times for heterozygotes (AG) and 1.90 times for homozygotes (AA) [PMID 17135278]

http://www.snpedia.com/index.php/Rs16969968

Pain[edit]

Rs6269-Not FTDNA Tested. rs6269
Rs4818-Not FTDNA Tested. rs4818

"rs4633","22","18330235","TC"rs4633

I am an rs4633 (C;T) (chr22 19,962,712 plus) higher risk for endometrial cancer

"rs4680","22","18331271","AG"rs4680 [1]

Rheumatoid Arthritis[edit]

Common variants at the promoter region of the APOM confer a risk of rheumatoid arthritis

"rs805297","6","31730585","--" The individuals with the rs805297 risk allele (A) at the promoter region showed a significantly lower level of APOM expression compared with those with the protective allele (C) homozygote. In the logistic regressions by the phenotype status, the homozygote risk genotype (A/A) consistently showed higher ORs than the heterozygote one (A/C) for the phenotype-positive RAs. These results indicate that APOM promoter polymorphisms are significantly associated with the susceptibility to RA.

Schizophrenia[edit]

My Schizophrenia Page

I have relatives with schizophrenia.

Tasting[edit]

I hated coke and coffee when I was young and chocolate had to have a great deal of sugar with it.

My Taste Page

Triglycerides[edit]

Triglyderides

Type II Diabetes[edit]

Type II Diabetes Page

Physical Features[edit]

Note: I have straight black hair[now white], brown eyes, and dark or olive brown skin and tan easily.

Physical Features In General[edit]

Physical Features In General

Hair Coloring[edit]

My Hair Color is Black
Hair Coloring Page

Skin Coloring[edit]

My Skin Color is Olive
Skin Coloring Page

Eye Color[edit]

My Eyes Are Brown
Eye Color Page

Baldness[edit]

NOTE: I have a full head of hair and was born in 1951.
Baldness Page

Neanderthal Similarities[edit]

Neanderthal Similarities

Haplogroups of mtDNA and yDNA[edit]

I am H3 Haplogroup mtDNA[edit]

I1000015-T6776C http://www.snpedia.com/index.php/I1000015
Rs2853508-A15326G http://www.snpedia.com/index.php/Rs2853508

HVR2 differences from CRS[edit]

263G
315.1C

CR differences from CRS[edit]

750G
1438G
4769G
6776C
7148C
8860G
5326G
15519C

HVR1 differences from CRS[edit]

16519C

Migration Route[edit]

http://www.facebook.com/photo.php?fbid=10150548277801457

I am J1c3d Subclade yDNA[edit]

HAPLOGROUP INFO
My Haplogroup Tests J1c3d
Positives

M267+=J1

P58+=J1c3

L147.1+=J1c3d

Negatives

M367-=Not J1c3a

M368-=Not J1c3a

M369-=Not J1c3b

L174-=Not J1c3d1

L222.2-=Not J1c3d2

L65.2-=Not J1c3d2a

I am not[edit]

I AM NOT

To Be Sorted[edit]

HMOX1[edit]

"rs2071747","22","34107185","GG"-MC

FGA Alleles 21-23[edit]

"rs2070022","4","155724398","GG"=MC
"rs2070016","4","155729764","AG"=TC=2nd

[PMID 20167083] Fibrinogen beta variants confer protection against coronary artery disease in a Greek case-control study

LPL Alleles 10-12[edit]

"rs13702","8","19868772","TT"=CC=MC
"rs15285","8","19868947","CC"=GG=MC
"rs1800590","8","19840951","TT"=MC
rs1801177 8 19849988 GG=MC?
"rs2197089","8","19870653","GG"=CC=RA
rs263 8 19857092 CC=MC

rs264 8 19857460 GG

rs270 8 19857956 CC

rs276 8 19858569 TT

rs283 8 19859378 CC

rs285 8 19859469 CC

rs291 8 19860132 TT

rs295 8 19860518 AA=MC

rs297 8 19860651 TT

rs301 8 19861214 TT=MC

rs316 8 19862716 CC

rs320 8 19863357 TT=MC
rs325 8 19863608 TT=MC

rs327 8 19863816 TT

rs331 8 19864685 GG=MC

HSD11B1[edit]

"rs2235543","1","207927291","CC"-MC
rs3753519 1 207942138 CC-MC
rs846910 1 207941877 GG-MC

[PMID 18611262] Genetic variation in candidate obesity genes ADRB2, ADRB3, GHRL, HSD11B1, IRS1, IRS2, and SHC1 and risk for breast cancer in the Cancer Prevention Study II

rs2236225 14 63978598 AA=TT Orientation minus Least Common

[PMID 19130090] rs1076991 C > T exerts a significant effect on promoter activity in vitro and along with rs2236225 G > A influences embryonic development.

"rs12194182","6","160754505","TC"

"rs11755393","6","34932614","AA" AG most common, AA second, Risk Allele G for systemic lupus erythematosus

http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs11755393

http://www.snpedia.com/index.php/Rs11755393

rs2232165 3 173648838 GG=CC Orientation minus rs2232165(C;C) normal

http://www.snpedia.com/index.php/Rs2232165

s27072, a SNP in the dopamine transporter SLC6A3 gene, has been associated with more severe symptoms upon alcohol withdrawal, such as seizures, in a study of 250 Caucasian alcohol-dependent patients. Two haplotypes appear to be tagged by this SNP and a neighbor, rs27048. The rs27072 polymorphism has been shown to be significantly associated with ADHD in clinical samples of Canadian children aged 6 to 16 [Feng et al., 2005] and the significant association was also reported by Ouellet-Morin et al. in a Canadian twin study, 2008 (Am. J. of Medical Genetics Part B, 147B:1442-1449 (2008). [PMID 18070248]
"rs27048","5","1465645","TT"

rs27048(T;T) normal

http://www.snpedia.com/index.php/Rs27048

"rs27072","5","1447522","TC"

rs27072(T;T) normal

http://www.snpedia.com/index.php/Rs27072

"rs1042173","17","25549137","AC"=GT Orientation minus

rs1042173(G;G) normal

rs1042173(G;T) normal

rs1042173(T;T) among alcoholics, likely to be heavier drinkers

rs1042173 is a SNP in the solute carrier family 6 (neurotransmitter transporter, serotonin), member 4 SLC6A4 gene.A study of 275 patients seeking treatment for alcoholism concluded that Caucasians of with the rs1042173(T;T) genotype consumed an average of 11.17 drinks per drinking day, compared with an average of 8.58 for carriers of a rs1042173(G) allele (p = 0.0034). While this held true for both men and women, this association was not seen in Hispanics. [PMID 19032574] [PMID 21247998] Pharmacogenetic Approach at the Serotonin Transporter Gene as a Method of Reducing the Severity of Alcohol Drinking

"rs1076560","11","112788898","CC"

In one study of Japanese males, rs1076560(A) alleles were 1.3 fold more associated with Alcoholism than the rs1076560(C) alleles. [PMID 17196743]

The DRD2 risk allele A was more prevalent in the alcoholic patients than in the healthy controls. These data identify rs1076560 as a potentially important variable in the development of alcoholism.

"rs1815739","11","66084671","TT"

[PMID 18043716] (T;T) under-represented in elite strength athletes, consistent with previous reports of impaired muscle performance.

rs1004819","1","67442801","AG=TC Orientation minus

rs1004819(C;T)1.5x risk for Crohn's disease in both Jewish and non-Jewish populations. [PMID 17068223]

http://www.snpedia.com/index.php/Rs1004819

rs1061170 1 194925860 TT (T;T) common/normal

rs1061170(C;C) 5.9x risk for AMD; higher mortality among nonagenarians

http://www.snpedia.com/index.php/Rs1061170

"rs7566605","2","118552495","CG" Weak, if any, association with obesity. http://www.snpedia.com/index.php/Rs7566605

"rs4986791","9","119515423","CC" Most Common Allele is C and risk allele is T.

http://www.snpedia.com/index.php/Rs4986791

"rs1143634","2","113306861","AG"=TC Orientation minus

rs1143634 increases susceptibility to Myasthenia gravis 1.29 times for heterozygotes (CT) and 4.63 times for homozygotes (TT) [PMID 9521608]

http://www.snpedia.com/index.php/Rs1143634

rs4986790 9 119515123 AA Most common haplotype among all populations and no disease associations

http://www.snpedia.com/index.php/Rs4986790

"rs1801275","16","27281901","GG" Highest Among Sub-Saharan African Populations

http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=1801275

http://www.snpedia.com/index.php/Rs1801275

"rs1048118","X","47368744","GG"

[PMID 20122735] Screening of DNA-variants in the properdin gene (CFP) in age-related macular degeneration (AMD)

http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=1048118

http://www.snpedia.com/index.php/Rs1048118

"rs6609257","X","43497652","GG"

I am an rs6609257 (G;G) (chrX 43,753,461 plus) and lefthanded from lefthanded parents with a lefthanded son.

[PMID 19028548] mentioned as potentially affecting white matter volume, sample size tiny, GG higher among Africans than Europeans and Mexicans.

16 healthy participants (14 males) took part. All participants were right-handed, Caucasian, and psychiatrically, medically andneurologically healthy. Ages ranged from 18 to 36 years (mean = 23.69, S.D. = 4.33) and participants had spent an average (S.D.) of 16.81 (2.64) years in full-time education.

http://www.snpedia.com/index.php/Rs6609257

"rs7885458","X","6230474","TT"

[PMID 19260141] gwas among adults residing on Korcula Island in Croatia, fibrinogen, the G allele associated with decreased fibrinogen levels.

"rs6048","X","138460946","AA" -Most Common

Gene variants associated with deep vein thrombosis.[PMID 18349091]

Updated analysis of gene variants associated with deep vein thrombosis.[PMID 20124536]

"rs2297480","1","153546106","TT"=AA Orientation minus

rs2297480 is a SNP in the FDPS gene, which encodes an enzyme in the mevalonate pathway and therefore might alter the response to amino-bisphonate (drug) treatment of postmenopausal osteoporosis.

A study of 234 Danish postmenopausal women treated for at least 2 years with amino-bisphonates concluded that rs2297480(C;C) homozygotes do not respond as successfully as (A;A) or (A;C) genotypes.[PMID 18687167]

http://www.snpedia.com/index.php/Rs2297480

"rs1741981","1","32529026","TC"
"rs2547547","5","140985871","AG"

Kaplan-Meier analysis showed that the combination of the T variant allele (CT+TT) of HDAC1 SNP rs1741981 and the homozygous TT variant allele of HDAC3 SNP rs2547547 was the most favorable prognostic factor.

http://www.snpedia.com/index.php/Rs1741981

http://www.snpedia.com/index.php/Rs2547547

rs11391 6 114368708 AA Orientation minus

[PMID 20731616] Combination of polymorphisms within the HDAC1 and HDAC3 gene predict tumor recurrence in hepatocellular carcinoma patients that have undergone transplant therapy

http://www.snpedia.com/index.php/Rs11391(T;T)

"rs320995","X","77414973","AA"=TT

Orientation-minus

Genotype Effect

rs320995(C;C)* ?

rs320995(C;T)* ?

rs320995(T;T)* ?

http://www.snpedia.com/index.php/Rs320995

[PMID 18829683] subjects without T-allele in SNP rs320995 had 3.1 times higher risk of asthma (Pobserved=0.00004)

"rs3764880","X","12834747","AA",

rs3764880(A;A)Magnitude: 1.6

References:2

1.2 - 1.8x increased tuberculosis risk rs3764880 is a SNP in the TLR8 gene, located on the X chromosome. rs3764880 is also known as Met1Val. A study of both Indonesian and Russian tuberculosis patients (and controls) concluded that the minor (A) allele of rs3764880 was associated with increased risk for tuberculosis. In the Indonesian population of 375 patients, the odds ratio was 1.8 (CI: 1.22.7); in the Russian population of 1,837 patients, the odds ratio was 1.2 (CI: 1.021.48); the combined evidence for association was p = 1.210e?3 610e?4. Note that the association was found primarily in males (although also to a lesser extent in homozygous females), presumably due to the presence of only one X chromosome in males.

http://www.snpedia.com/index.php/Rs3764880

"rs3397","1","12189879","--"

Those individuals carrying the variant TNFRSF1B rs3397 C allele showed a statistically significant reduction in the probability of developing Crohn disease with penetrating behavior, as compared with those carrying the T allele (OR = 0.62, 95% CI = 0.40–0.95, P = .03).

http://www.snpedia.com/index.php/Rs3397

"rs6684865","1","2536089","AA"

rs6684865 has been reported in a large study to be associated with rheumatoid arthritis.

Rs6684865(A;A) 0 1.5x risk

Rs6684865(A;G) 1.2x risk

Rs6684865(G;G) normal

http://www.snpedia.com/index.php/Rs6684865

rs11701 14 20231893 TG

The common form at this site in most populations is rs11701(T), and the variant form is rs11701(G). Having at least one copy of this variant form, rs11701(G), has been associated with an increased incidence of ALS in Scottish and Irish populations studied, but not in populations from the U.S., Sweden, or England. [PMID 16501576] rs11701 In Irish amyotrophic lateral sclerosis patients, there was a significant allelic association with the rs11701 SNP & a new mutation (K40I) that potentially inhibits angiogenin function. The common form at this site in most populations is rs11701(T), and the variant form is rs11701(G). Having at least one copy of this variant form, rs11701(G), has been associated with an increased incidence of ALS in Scottish and Irish populations studied, but not in populations from the U.S., Sweden, or England. [PMID 16501576] rs11701 In Irish amyotrophic lateral sclerosis patients, there was a significant allelic association with the rs11701 SNP & a new mutation (K40I) that potentially inhibits angiogenin function.

"rs10239794","7","153836827","TC" (C;T)=1.3x risk for ALS

http://www.snpedia.com/index.php/Rs10239794

"rs9897526","17","39782466","GG" G is most common allele. Common variants (rs9897526, rs34424835, and rs850713) and haplotypes were significantly associated with a reduction in age at onset and a shorter survival after onset of ALS in both the Belgian and the Dutch studies.

rs6718526 2 160922421 TC