Verify relationship in paternal line, with known terminal SNP and private „novel“ SNPs from NGS

If you wanted to compare the Y-DNA of two men, you used Y-STR tests with as many markers as possible. If one or more NGS (Next Generation Sequencing) are available, a new method can be used to determine the relationship of two men in a purely paternal line using “young” SNPs. Your youngest SNPs are those that have only been detected in your sample. These are called “Novel SNPs” or “Private SNPs”.

This method is made possible by the company and the possibility to actually test any SNP that can be tested with the Sanger method for little money after you “wish” for it. However, this variant only works if the number of private SNPs or SNPs in the terminal block is not too high, as the costs for this increase with the number of SNPs to be tested.

  1. After you’ve made an NGS, you should make some preparations.
  2. Once the preparations have been made, another tester can quickly and inexpensively determine the relationship and determine the most recent common Y-SNP (New Common Terminal SNP).

1. Preparations after NGS test.

1.1 Add SNPs from NGS to list.

A reasonable sorting of these Y-SNPs by age is only possible if there are several branches due to several testers in this Y-Haplogroup. Fig. 1 shows the SNPs of BY25359>BY25363>BY35090>Y130323 in four blocks. The order of the SNPs within the blocks cannot be determined until another branch is added by a tester being positive for only part of the SNPs. The most recent SNPs are in block A, the oldest in block D.

fig. 1: List of SNPs, I-L38 >> BY25359
fig. 1: List of SNPs, I-L38 >> BY25359

Create a list (spreadsheet) of your “youngest” SNPs. As columns you take: Position hg38, ancestral allele, derived allele, region, SNP-name, Y-Haplogroup, YSEQ and if you like more columns, with important information for you. In the column “Region” you can enter the following formula (column A = position hg38):


Column YSEQ:

  • YSEQ only recommends testing SNPs outside the hg38 regions PAR1, CEN, DYZ19, PostPali and PAR2 as these are not useful for phylogenetic studies. SNPs from other regions can be marked as “wish SNP!”.
  • Mark SNPs from the hg38 regions PAR1, CEN, DYZ19, PostPali and PAR2 as “not orderable”.
  • Use the search to check which SNPs are already “orderable”. Please note that some SNPs have several names (e.g. BY35090 = Y129739).

1.2 Superior Strategy and “Wish” SNPs to Order

This method can be used in different cases. It makes sense to first think about the individual strategy and to consider which SNPs should be orderable for your studies. In most cases, this should be the private variants (Block A, Fig.1), as well as variants from the terminal block (Block B, Fig.2).

1.2.1 Wish a SNP

„Wish a SNP“ tells YSEQ which SNPs you wish to be included in the assortment. You only have to consider that these are in the testable ranges.

  • Choose the „Haplogroup“ and „Reference Sequence“ (hg38/GRCh38) from Available Options.
  • >>Add to Cart.<<
  • Update of total number in shopping cart.
  • >>Checkout<<
  • Insert following information at „Add Comments About Your Order”:
    • Name of desired SNP (if named)
    • Position hg38
    • Ancestral allele
    • Derived allele
    • Observed haplogroup
  • Order

A few days later you should receive the information which SNPs are available, and which are not. Add this information to your list.

1.2.2 Wish a Panel

If you have more than seven SNPs, you can use „Wish a Panel“ to bundle the SNPs into packages. This simplifies the ordering process compared to ordering individual SNPs.

  • Choose „Haplogroup“ in Options
  • >>Add to Cart.<<
  • Update of total number in shopping cart.
  • >>Checkout<<
  • Insert following information at „Add Comments About Your Order”:
    • name of the desired panel
    • List of SNPs
    • a short description about the panel
    • who should test for this panel.
  • Order

A few days later you receive confirmation that the panel can be ordered.

fig. 2: Verify relationship in paternal line

2. Order SNPs

2.1 Verify paternal relationship

  1. It is now possible to test a single SNP and thus determine a relationship in a purely paternal line. Take either a terminal SNP or an SNP from an older block.
  2. Be careful. If a terminal SNP is too young, the MRCA (Most Recent Common Ancestor) may be older than the tested SNP. Whether this is the case can be checked by testing an SNP of an older block.

2.2 Determining the degree of relationship

  1. Once it has been established that there is a relationship, the private SNPs should be tested. Of these, some should be positive and others negative. However, it is also possible that none or all of them are positive. The degree of kinship can be estimated from the number of SNPs, which are not shared.
  2. If all private SNPs are negative, it is possible that some of the terminal SNPs are also negative. This should be checked.

3. Advantages of this method

  • Simplest and cheapest solution for verifying Y relationship. (if “young” terminals SNP known based on NGS test and low number of philoequivalent and private SNPs.
  • Almost any SNP can be ordered “Wish a SNP”.
  • Create custom panels.
  • Parts of blocks of private “Novel” or philoequivalent SNPs (e.g. block terminals SNPs) without further NGS, for more detailed determination of a Y relationship.
  • Sample is stored for upgrades.
  • Buy an empty DNA Sample Kit and order the product of your choice as soon as the kit arrives in the lab.

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