Initial Steps
The first steps to be carried out on your DNA journey are as follows:
1. Create an account and order your FREE test kit (the 50c charge is for verification purposes and it is refunded).
2. Follow the test kit instructions and return your sample as instructed.
3. Through your website account, you will receive genetic ancestry percentages and raw genetic data that you can download if you want to do further analyses using external tools. It generally takes anywhere between 4-8 weeks for results to get back to you after the lab receives the kit (this may take longer if the lab is backed up).
What is a DNA test?
A DNA test or genetic test is a testing method used to determine genetic relationships amongst people or determine someone’s genetic ancestry. Since every cell in an individual’s body contains DNA, material such as a saliva sample can be used to extract one’s DNA, which can then be prepared for analysis. DNA, or deoxyribonucleic acid, is a molecule that contains the biological instructions that help to define an individual. DNA is hereditary and it is passed on from the parents to the offspring. Because DNA (and its variations) can be passed down from generation to generation, one’s genetic ancestry can be traced back to multiple generations ago.
If you want to learn more about DNA and the human genome in general, see this page: https://www.genome.gov/About-Genomics/Introduction-to-Genomics#four
If you want to learn more about DNA and the human genome in general, see this page: https://www.genome.gov/About-Genomics/Introduction-to-Genomics#four
Spectrum Genetic Data
The genome is divided into 23 pairs of chromosomes (22 pairs of autosomal chromosomes, 1 pair of sex chromosomes) that are made up of more than 3 billion building blocks called nucleotide bases (A, T, C and G). Whole genome sequencing is the procedure that determines the order of nucleotide bases in the genome of a person at a single time. Typically, a generated sequence is compared to an accepted representation of the human genome (called the reference sequence) to detect any variant nucleotides. The reference sequence is a general framework and it is not the sequence of a single individual.
The genetic data that a participant obtains from Spectrum is called low-pass whole genome sequencing data and it is obtained by comparing the participants’ sequence to the GRCh38 v6.0 human reference sequence. The standard format for storing sequence variations is called the variant call format (VCF). Because the file name suffix is .vcf, phones and computers may translate the data file as a contact card file (https://www.lifewire.com/vcf-file-2622845) which one has to be mindful of.
There are a lot of paid and free DNA websites that allow uploading of external data. Most of these sites seek to extract information on health/wellness and/or ancestry. These websites require that the data be in a particular format. Examples include:
• GEDmatch – provides ancestry tools and accepts data in 23andMe, AncestryDNA or FamilyTreeDNA formats.
• Genomelink – can provide an ancestry report, physical trait information or wellness tips. Genomelink accepts data in 23andMe, AncestryDNA or MyHeritage formats.
• Nebula Genomics – provides trait reports and other information about a user’s genome. The file formats accepted are 23andMe or AncestryDNA.
• Genetic Genie – allows for easy interpretation of a user’s genetic information. File formats accepted include 23andMe, AncestryDNA, FamilyTreeDNA, MyHeritage, LivingDNA, whole genome/exome sequencing VCF files, etc.
• Sequencing.com – provides ancestry and health reports. Accepted file formats include 23andMe, AncestryDNA, FamilyTreeDNA, MyHeritage, LivingDNA, whole genome/exome sequencing VCF files, etc.
• etc.
• Genomelink – can provide an ancestry report, physical trait information or wellness tips. Genomelink accepts data in 23andMe, AncestryDNA or MyHeritage formats.
• Nebula Genomics – provides trait reports and other information about a user’s genome. The file formats accepted are 23andMe or AncestryDNA.
• Genetic Genie – allows for easy interpretation of a user’s genetic information. File formats accepted include 23andMe, AncestryDNA, FamilyTreeDNA, MyHeritage, LivingDNA, whole genome/exome sequencing VCF files, etc.
• Sequencing.com – provides ancestry and health reports. Accepted file formats include 23andMe, AncestryDNA, FamilyTreeDNA, MyHeritage, LivingDNA, whole genome/exome sequencing VCF files, etc.
• etc.
Spectrum participants have the right to download their data and upload to any one of the available DNA websites. However, we advise caution and hope that participants are fully aware of the risks of such uploads before proceeding (read all necessary Terms and Conditions). Given that current Spectrum data are VCF files, there is a smaller set of websites that a participant can upload their data to e.g. Sequencing.com. In the future, we will provide 23andMe format data, which will allow participants to upload to a broader set of DNA websites. If you want to convert your Spectrum VCF file to 23andMe format, follow these steps:
• Download the bioinformatics software PLINK (https://www.cog-genomics.org/plink/)
• In your command line, run the following command:
plink --vcf [name of spectrum vcf file] --snps-only --recode 23 --out new23andMeFile
• In your command line, run the following command:
plink --vcf [name of spectrum vcf file] --snps-only --recode 23 --out new23andMeFile
Spectrum Genetic Ancestry Estimates
A person’s DNA is a combination of pieces that have been derived from one or many ancestral populations. To assign ancestry estimates, reference population sets, which are proxies of ancestral populations, need to be assembled first. The reference population sets have DNA of people whose families have lived in a certain part of the world for many, many generations. A Spectrum participant’s DNA pieces are compared to each of the reference population groups to see which group the participant’s DNA resembles the most. The ethnicity estimates for each piece are summed up over the entire genome of the individual.
The genetic ancestry estimates that Spectrum provides are calculated using the Gencove Ancestry Deconvolution procedure (https://resources.gencove.com/hc/en-us/articles/7267123074587-Gencove-Ancestry-Decovolution). The reference population sets that Gencove uses for the ancestry estimation are listed here: https://resources.gencove.com/hc/en-us/articles/7267880409883-Human-Ancestry-Reference-Populations.
The genetic ancestry estimates that Spectrum provides are calculated using the Gencove Ancestry Deconvolution procedure (https://resources.gencove.com/hc/en-us/articles/7267123074587-Gencove-Ancestry-Decovolution). The reference population sets that Gencove uses for the ancestry estimation are listed here: https://resources.gencove.com/hc/en-us/articles/7267880409883-Human-Ancestry-Reference-Populations.
