23andMe

  • Opus 23 now supports multiple platforms

    The recent change in the reporting done by 23andMe from the V4 to V5 chip has thrown things into a bit of a dither. The earlier V4 SNP array was more robust, at least with SNPs of interest to those who work in nutrigenomics. For example, V4 reported over ten MAO SNPs of nutritional interest, whist V5 reports none. To circumvent the problem, I’ve recoded Opus 23 to allow the clinician to upload, singly or in combination, data files from 23andMe (V3, V4, V5), Ancestry DNA and the ‘Export to Promethease’ file available from Genos. To move Opus in this direction required a lot of recoding and I thank all our users for their support and patience.

    The first time you load an existing client profile into Opus it will take a bit longer to process the file. This is because they are being upgraded to the new data storage system. After that they should load as usual. Manage->Profiles->Append Raw Data to Current Client will take you to the BLENDER app,which allows you to merge raw data files. This will only be important as people begin to use Ancestry DNA, perhaps in combination with 23andMe V5. Since almost everyone currently in Opus is 23andMe V4 you really don’t need to do anything.

    The ‘Upload New Client Raw Data’ script has been extensively re-written. You still upload a ZIP file, but the script will identify the platform (V3/V4, V5, Ancestry DNA) and let you know. It also now features and extra screen so that you can verify/validate your form input before doing the final upload. Hopefully this will cut down on people contacting us having uploaded the same client twice.

    Uploading and merging  V5 and Ancestry DNA client data have about 74% of Opus-curated snps, while the prior V4 has about 79% coverage.

    If you do upload Ancestry DNA data, be advised that Ancestry names its raw data files in a non-unique manner, usually something like ‘dna-data-2017-09-03.zip’. This blunts the ability of the program to warn you that you are using the same data file on two different clients. You should rename the client raw data ZIP file on your hard drive to something unique (we recommend replacing Ancestry DNA filename with the client’s first and last initials and date of birth; in this case ‘dna-data-2017-09-03.zip’ might become ‘MG-11-22-1956.zip.’ But you can use any system you wish as long as each uploaded filename is unique.

    It looks like the best short term solution will be to have the client do BOTH 23andme V5 and Ancestry.  Opus 23  now allows you to sequentially upload the raw data and merge it. We will eventually move towards a dedicated chip. However this change from v4 to v5 caught everyone (not just Opus/Datapunk) flat-footed as to the huge drop in clinically significant SNPs that are reported in v5. Even in the best of circumstances it will be weeks and months until a specialized chip will become available. However, in the meantime, piggybacking 23andMe v5 with Ancestry DNA appears to be not all that bad of a temporary fix. Many of these SNP panels are having significant price drops, so having the client do bot 23andMe V5 and Ancestry DNA should not be prohibitively expensive.

     

    In Other News

    You can now compare V5, V4, Genos Promethease export, and Ancestry data as compared to the core 2600 Opus snps. Just log in, click the ‘Informatics’ pull down, the select ‘Tools/ Extras’ and “Platform Comparisons’. Table is searchable, sortable and filterable.

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  • Protection against risk of Parkinson’s disease

    Parkinson’s disease was described in 1817 by Dr James Parkinson, who published an essay reporting six cases of ‘paralysis agitans’ (the disorder that was later renamed after Parkinson). He described the characteristic resting tremor, abnormal posture and gait, paralysis and diminished muscle strength, and the way that the disease progresses over time. [1]

    Since the advent of genetic testing several genes have been found to be associated with Parkinson’s disease (PD), resulting in various classifications. Autosomal dominant Parkinson disease type 8 (PARK8) is caused by heterozygous mutation in LRRK2, the gene encoding the dardarin protein. [2] The G2019S variant is one of the most common genetic causes of PD. Although the clinical motor signs of PD in carriers of the G2019S mutation are largely typical, an earlier age at onset of motor symptoms has been reported in some studies. [3]

    The word dardarin was taken from a Basque word for tremor, as the gene was first identified in families from England and the north of Spain. Mutations in LRRK2 are the most common known cause of familial and sporadic PD, accounting for approximately 5% of individuals with a family history of the disease and 3% of sporadic cases. They account for up to 10% of autosomal dominant familial and 3.6% of sporadic PD. More than 40 different variants, almost all missense, have been found. Seven seem to be proven pathogenic mutations, and are clustered in functionally important regions which are highly conserved through evolution. [4]

    23andMe carried out a privately-funded genome-wide association study (GWAS) to search for novel genetic variants associated with PD. The results, which were published in PLOS in 2011, replicated existing associations and discovered two novel variants. [5] In addition, 23andMe researched genes conferring protection on those with high-risk genes. [6] They found that of the approximately 1 in 10,000 people who have the G2019S  variant, those who also had a mutation in SGK1 were found to have a lower risk of PD than those with just the G2019S variant, conferring protection against the increased risk of PD. [7]

    Other causes of, or factors contributing to PD include pesticide exposure, [8] head trauma, medication, prolonged oxidative stress from infection or high homocysteine. Genetic factors include increased function of MAOB enzymes, high histamine from HNMT mutations, elevated L-dopa from DDC mutations or B6 deficiency. The Opus 23 software contains algorithms for Parkinson’s disease associated with some of these genetic causes, risk or contributory factors found in the 23andMe raw data. A new algorithm added to the Opus 23 Lumen app looks for both the LRRK2 G2019S and the SGK1 variants to assess for both risk of PD and protection from the risk genotype, and lists natural agents associated with gene function.

    References:

    1. Parkinson J. An essay on the shaking palsy. London: Sherwood, Neely and Jones; 1817.
    2. Kachergus J, Mata IF, Hulihan M, et. al. Identification of a novel LRRK2 mutation linked to autosomal dominant parkinsonism: evidence of a common founder  across European populations. Am J Hum Genet. 2005 Apr;76(4):672-80. Epub 2005 Feb 22. PMCID: PMC1199304.
    3. Thaler A, Mirelman A, Gurevich T,  et. al. Lower cognitive performance in healthy G2019S LRRK2 mutation carriers. Neurology. 2012 Sep 4;79(10):1027-32. PMCID: PMC3430708.
    4. Davie CA (2008). “A review of Parkinson’s disease”. Br. Med. Bull. 86 (1): 109–27. PMID 18398010
    5. Do CB, Tung JY, Dorfman E, et. al. Web-based genome-wide association study identifies two novel loci and a substantial genetic component for Parkinson’s disease. PLoS Genet. 2011 Jun;7(6):e1002141. PMCID: PMC3121750
    6. 23andMe Blog: 23andMe Discovers Genetic Variant That May Protect Those at High Risk for Parkinson’s Disease. Accessed Aug 28, 2016.
    7. Polymorphisms associated with Parkinson’s disease. Patent US8187811 B2.
    8. Van Maele-Fabry G, Hoet P, Vilain F, Lison D. Occupational exposure to pesticides and Parkinson’s disease: a systematic review and meta-analysis of cohort studies. Environ Int. October 2012, 46: 30–43. PMID: 22698719.

     

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  • Kava-kava for panic attacks

    A 2008 paper by Thoeringer et. al., published in the Journal of Neural Transmission [1] described a study of 238 adult Caucasian patients recruited from an Anxiety Disorders Outpatient Clinic in Europe presenting various anxiety disorders, including panic disorder, agoraphobia, social phobia and generalized anxiety disorder. As there are many genetic studies linking the GABA system to anxiety disorders and related personality traits, the patients were genotyped for various polymorphisms in the SLC6A1 (GABA transporter 1), along with 267 controls without anxiety disorder.

    Five polymorphisms in SLC6A1 or in the promoter region were found to be nominally associated with anxiety disorders. Although none were statistically significant alone, the authors found a significant combined effect of all investigated polymorphisms, which strongly suggested a major role of SLC6A1 in the genetic susceptibility of pathological anxiety. Looking at patients with panic disorder, those with the most severe panic disorder were significantly more likely than controls to have two related polymorphisms in the SLC6A1.

    GABA (gamma-aminobutyric acid) is a neurotransmitter that decreases activity in the neurons of the brain and inhibits the excitability of nerve cells. Drugs that block the GABA transporter molecule inhibit the removal of GABA from the nerve synapses, thereby prolonging the action of GABA. Tiagabine, a selective GABA transporter 1 blocker, is used as an antiepileptic, but has off-label use for anxiety disorder. This is thought to be due to the augmentation of GABA function as a neurotransmitter in the brain. This drug has side-effects, however, and other methods of reducing panic disorder have been investigated.

    Kava-kava (Piper methysticum) is a traditional plant-based medicine found in the Western Pacific region which has been shown to reduce anxiety. Kava-kava is legal in most countries, and is generally safe when the root from a ‘noble’ cultivar is used. A study of kava-kava for anxiety reduction using the Hamilton Anxiety Rating Scale (HAMA) as the primary outcome found that patients with generalized anxiety disorder who had polymorphisms in SLC6A1 and in the 5′ flanking region potentially responded to kava-kava supplementation with a more significant reduction in HAMA rating than in patients without the polymorphisms. [2] Treatment consisted of tablets standardized to contain 60 mg of  kavalactones per tablet for a total daily dose of 120 mg of kavalactones for the first 3-week controlled phase, being titrated to 240 mg of kavalactones in nonresponse at the 3-week mark for the second 3-week controlled phase, or placebo.

    An algorithm in the Lumen app in Opus 23 determines how many relevant SNPs a client has in SLC6A1 that are reported in their 23andMe raw data, and which may make treatment with kava-kava more effective in reducing anxiety disorder and panic symptoms.

    References:

    1. Thoeringer, C.K., Ripke, S., Unschuld, P.G. et al. The GABA transporter 1 (SLC6A1): a novel candidate gene for anxiety disorders. J Neural Transm (2009) 116: 649. doi:10.1007/s00702-008-0075-y. PMCID: PMC2694916
    2. Sarris J, Stough C, Bousman CA, et.al. Kava in the treatment of generalized anxiety disorder: a double-blind, randomized, placebo-controlled study. J Clin Psychopharmacol. 2013 Oct;33(5):643-8. doi: 10.1097/JCP.0b013e318291be67. PMID: 23635869
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  • Genetic factors in depression, neuroticism and well-being

    Raining DNA

    Depressive and neurotic behaviours have many potential triggers and contributory factors, but few associated genetic variants have been found, most likely due to the large numbers of subjects needed: Genome-Wide Association Studies (GWAS) require large sample sizes to have sufficient statistical power, which is often achieved by aggregating results in multiple cohorts in a meta-analysis. A paper to be published in Nature Genetics in June 2016 [1] reports on the results of combining several large conducted on three phenotypes:

    • subjective well-being (n = 298,420)
    • depressive symptoms (n = 161,460)
    • neuroticism (n = 170,911).

    Using a meta-analysis on publicly available results from a study performed by the Psychiatric Genomics Consortium together with new results from analyses of the initial release of UK Biobank (UKB) data and the Resource for Genetic Epidemiology Research on Aging cohort, two variants were found to be associated with depressive symptoms. In the UKB cohort  the researchers measured depressive symptoms by combining responses to two questions asked of 23andMe customers with European ancestry. The questionnaire asked about the frequency in the past 2 weeks with which the respondent experienced feelings of low levels of enthusiasm or disinterest, and feelings of depression or hopelessness. The other cohorts included case-control data on major depressive disorder.

    According to Eysenck and Eysenck, [2] neurotic people become easily nervous or upset due to a lowered activation threshold in the sympathetic nervous system, and experience emotional instability in the form of fight-or-flight symptoms resulting from apparently minor stressors. Using twin studies, Eysenck concluded that, “the factor of neuroticism is not a statistical artefact, but constitutes a biological unit which is inherited as a whole….neurotic predisposition is to a large extent hereditarily determined.” [3]

    To analyse this potential genetic association with neuroticism (n = 170,911), the research combined statistics from a published study by the Genetics of Personality Consortium (GPC) with results from a new analysis of UKB data. Eleven variants were found to be associated with neuroticism. The GPC data harmonised different neuroticism batteries, and in the UKB cohort the measure was the respondent’s score on a 12-item version of the Eysenck Personality Inventory Neuroticism.

    This was also the first study to find SNPS that have a significant association with subjective well-being, of which the researchers identified three relevant variants. Questionnaires measured both positive affect (a state of pleasant arousal enthusiasm) and life satisfaction, even though these are different concepts of well-being.

    The SNPs in this study were found mainly in loci regulating expression in tissues of the central nervous system, adrenals or pancreas, including CSE1L , DCC , HNRNPA1P1, KSR2, MTCH2 NMUR2  PAFAH1B1 and RAPGEF6. Previous studies had found a relevant variant in MAGI1, accounting for approximately 15% of the variability in neuroticism, [4] as well as SNPs in TMPRSS9 and GRIN2B. [5]

    23andMe typically reports on up to six of the SNPs in this study related to neuroticism and two related to depression. Two algorithms in the Opus 23 Pro [6] Lumen app can determine the relevant genotypes for these phenotypes from SNPs available in 23andMe raw data.

    References:

    1. Okbay A, Baselmans BM, De Neve JE, et. al. Genetic variants associated with subjective well-being, depressive symptoms, and neuroticism identified through genome-wide analyses. Nat Genet. 2016 Jun;48(6):624-33. doi:10.1038/ng.3552. PMID: 27089181.
    2. Eysenck, H. J. & Eysenck, S. B. G. (1969). Personality Structure and Measurement. London: Routledge.
    3. The Journal of Mental Health, July 1951, Vol. XCVII, “The Inheritance of Neuroticism: An Experimental Study”, H. J. Eysenck and D. B. Prell, p. 402.
    4. Genetics of Personality Consortium, de Moor MH, van den Berg SM, et. al. Meta-analysis of Genome-wide Association Studies for Neuroticism, and the Polygenic Association With Major Depressive Disorder. JAMA Psychiatry. 2015 Jul;72(7):642-50. doi:10.1001/jamapsychiatry.2015.0554. [PMID: 25993607].
    5. Aragam N, Wang KS, Anderson JL, Liu X. TMPRSS9 and GRIN2B are associated with neuroticism: a genome-wide association study in a European sample. J Mol Neurosci. 2013 Jun;50(2):250-6. doi: 10.1007/s12031-012-9931-1. [PMID: 23229837].
    6. Opus 23 Pro software by Dr Peter D’Adamo.
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  • Decoding 23andMe ‘i’ Numbers

    23andMe currently reports over 600,000 SNPs in the genome explorer, which are analyzed by their custom 2014 v4 chip. The process used is genotyping, rather than sequencing. The former is cheaper and quicker, and targets specific parts of the genome that are known to have variants in some or many people; the latter is used to find out the code of nucleotide base pairs in a sequence (or continuous stretch) of DNA, the exome (the coding part of DNA), or all the DNA in the whole genome.

    Genotyping does not report on all possible insertions or deletions. In general, it only reports small changes, spanning only one or a few bases. Sequencing will check whether all the DNA code in a region is found in the usual configuration or whether there are any unknown insertions or deletions.

    23andMe doesn’t test for all the SNPs they report on, but might impute variants present on larger chips or in sequencing analysis, using a statistical method that allows researchers to fill in missing data. This may be the reason 23andMe say “This data has undergone a general quality review, however only a subset of markers have been individually validated for accuracy.” [1]

    An example of this might be RhD blood group status: If you have a double deletion (DD) at “i4001527” you are RhD negative, if you don’t have the double deletion (DI or II) you are Rh positive. This number is available from a search in the 23andMe explorer, but is not found in the raw data can be downloaded in an ASCII text file and used for uploading to Opus23 Pro.

    Most of the numbers representing SNPs in the 23andMe raw data begin with ‘rs’, which are reference SNP identifiers, or reference SNP cluster IDs. [2] These rsIDs are assigned and managed by dbSNP, the official database for short genetic variations. However some numbers in the 23andMe raw data begin with ‘i’, which is an internal number assigned by 23andMe for testing locations on the genome for various reasons. This includes SNPs where the probes used differ from the reference sequence.[3] Some ‘i’ numbers are SNPs that don’t have rsIDs: 23andMe maps the i-number to the chromosome position, and internally they map this number to anything else they need to know about the SNPs to put it on a chip (many of these SNPs come from the custom portion of the genotyping array). Other ‘i’ numbers relate to SNPs that could highlight a genetic mutation in a user which is related to significant health risks or genetic conditions. The FDA don’t want users to be able to find out that they have these problems without genetic counselling, except for under specific circumstances where the user has made a declaration that they understand the consequences of accessing this data and what it might mean. The FDA are currently seeking medical opinion on situations where genetic test results might be available directly to the user. Comments can be submitted online  to the FDA by March 31st 2016. All submissions must include reference to: “Docket No.  FDA-2015-N-4809 for `Patient and Medical Professional Perspectives on the Return of Genetic Test Results; Public Workshop; Request for Comments.’”

    How does Opus23 Pro deal with ‘i’ numbers?

    Opus23 Pro curators use the genomic location linked with the coded ‘i’ numbers to find the rsID (if one exists), and if relevant, the ‘i’ numbers are added to the Opus23 Pro SNP database, and a lookup is performed by the software when analysing a client’s raw data. The ‘i’ numbers are linked with the rsID in the software, and this gives the practitioner a reference for further research in published medical literature. Any significant genetic risk factors can be added to the client report and explained to the patient, along with genetic counselling as necessary.

    References:

    1. Web page: “How 23andMe Reports Genotypes” https://customercare.23andme.com/hc/en-us/articles/212883677-How-23andMe-Reports-Genotypes.  Accessed 3/5/16
    2. The NCBI Handbook [Internet]. 2nd edition. Bethesda (MD): National Center for Biotechnology Information (US); 2013-. Accessed 3/5/16

    3. 23andMe forum “23andMe upgrading to NCBI Build 37 coordinates on Aug. 1” https://www.23andme.com/you/community/thread/14308/6/ Accessed 3/5/16
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