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dna.reinyday.com - Genealogical DNA Testing
Background. DYS464 (also written as DYS 464, DYS#464, and DYS# 464) is a commonly tested DNA marker, which is very useful for genealogical DNA testing. DNA Heritage offered a wonderful "Masterclass" tutorial on primer pairs and multiplexes, which can help you visualize how a DNA test is conducted. The lab uses a "primer" to mark the beginning of a repeat sequence (STR). Then a laser is used to create a fluorescence peak.
The result is an electropherogram, which is a plot of fluorescence units over time.
Marker DYS464 appears to be a rapidly changing Y chromosome marker and is a multi-copy marker. DYS464 occurs at least four times near the center of the Y-chromosome. The first four copies are called: DYS464a, DYS464b, DYS464c, DYS464d. Marker DYS464 is also known to occur more than four times, generally in African lineages of Haplogroup E. Additional copies of DYS464 are called: DYS464e, DYS464f, and so forth... DYS464 has an observed range between 9 to 20 inclusive.
When testing a random sample of 679 males for DYS464, scientists have found that the result 15,15,17,17 occurred in 10.6% of those tested, 15,15,16,17 occurred in 7.5% of the samples, and all the other results occurred less than 5% of the time, with over half these results only occurring once. This illustrates that Marker DYS464 is valuable in differentiating unrelated persons or splits in branches that have failed to show variation with other markers in the panel. In fact DYS 464 alone has a greater ability to split then the first 12 markers combined.
[from Family Tree DNA's Facts & Genes, volume 3, issue 2 (March 2004)]
Electropherogram Interpretation Discrepancy. I had my uncle and his uncle tested at two different labs. The results were identical (as expected) except for DYS464. I personally believe that the results were identical for DYS464, but interpreted differently by the labs. DNA Heritage found that my uncle had six values for DYS464, while Family Tree DNA found that my grand uncle had four values for DYS464.
DNA Heritage (which has since been bought by Family Tree DNA) was kind enough to provide me with my electropherograms for DYS464 and to grant permission for me to post them here. My uncle's test for DYS464 was run three times to be sure of the unusual results. Below are the results of each run.
Because my plots show three peaks of varying heights, DNA Heritage concluded that my values are 12, 12, 15, 15, 15, 16. Specifically they looked at the peak for 16 and noted that the peak for 12 is twice as high and the peak for 15 is three times as high. So they determined that there are twice as many "12" values and three times as many "15" values as there are "16" values.
Family Tree DNA would not provide an electropherogram nor disclose peak-height information. Family Tree DNA concluded that my values are 12, 15, 15, 16. Values are always given in numberical order.
Three years later, I tested an additional person with Family Tree DNA to see if he was a family member. This man (with identical surname and living in the same ancestral village in Europe) turned out to be a 64/67 match and was reported with the same four values as the other Family Tree DNA test. After a series of insistent e-mails back and forth with the company, Family Tree DNA provided a free DYS464X upgrade test. DYS464X was offered by Thomas Krahn, who had partnered his lab DNA-Fingerprint with Family Tree DNA. The labs have since split and Krahn now offered his sequencing through YSEQ (which I personally recommend).
As a result of the DYS464X tests through DNA-Fingerprint, both Family Tree DNA tests were adjusted to match the DNA Heritage test. Now all three tests show the same six values for DYS464. Krahn informed me that my family also has an unusal result for DYF399, but would not provide the results without me ordering the test (though the test had already been run), which I still have not done. If you would like to pay for that test, you can PayPal $24 to: paypal "at" reinyday.com
David Reynolds details his non-matching DYS464 tests results from Family Tree DNA and DNA-Fingerprint in the Spetember 2005 mailing list post "Another set of extended DYS464, DYF385S1, DYF399S1 results". David is Haplogroup R1b.
Jim T. explicates his non-matching DYS464 tests results from Family Tree DNA and DNA-Fingerprint in the Spetember 2005 mailing list post "Another set of extended DYS464, DYF385S1, DYF399S1 results". He has since tested at a third lab and then retested at Family Tree DNA, which decided the other two labs were correct and changed their results. Jim is Haplogroup R1b.
Chris Meeks alerts project administrators about DYS464 problems from Family Tree DNA in his April 2007 mailing list post "DYS 464". Chris's group of misreported results are Haplogroup R1b1c.
Vincent Vizachero mentions incorrect results from Family Tree DNA for DYS464 for haplogroup R1b1c in his April 2007 mailing list post "DYS 464".
Alfred A. Aburto Jr. explains Family Tree DNA revising his DYS464 results in his April 2007 mailing list post "DYS 464". Alfred is Haplogroup J2a1*.
Joe Fox mentions non-matching DYS464 tests results from Family Tree DNA and DNA-Fingerprint in his April 2007 mailing list post "DYS 464". The results he refers to are Haplogroup R1b1c9a.
Haplogroups: Please note that almost all of the people with discrepencies on DYS464 that I have been in touch wih have been Haplogroup R1b. My mismatched results are the only instance that I know of for Haplogroup R1a. The Aburto results linked above are the only instance that I know of for Haplogroup J2a1*.
Family Tree DNA reported that additional DYS464 markers are most commonly seen in African lineages of Haplogroup E.
Number of Alleles: The term allele refers to the possible results for a given location (known as a loci or a marker) on a chromosome. The possible alleles (number of repeats, i.e. test results) for DYS464 range from 9 to 20. My tests show three unique alleles (12, 15, and 16) which are interpreted, based on the peak heights shown in the electropherograms, to represent 4 or 6 instances of this marker. All of the scientific papers I have read, and all of the forensic scientists I have spoken with, have said that there are a maximum of four unique alleles for DYS464. However, ySearch lists at least one individual with five unique alleles: 12, 14, 15, 16, and 17; he tested with Family Tree DNA (which owns ySearch).
Infertility: The absence of DYS464 may reveal infertility. See the paper Inadvertent diagnosis of male infertility through genealogical DNA testing or the article DNA-based genealogy test reveals infertility.
DYS 464 [infertility] is an October 2005 mailing list post that provides a good general explanation of the connection between DYS 464 and infertility.
DYS464X: YSEQ (previously DNA-Fingerprint) offers a DYS464X (Extended) Test, which uses a special method of testing the DYS464 STR alleles (with different fluorescent dyes) that benefits people in Haplogroup R1b.
Of the 14 STRs studied, "... DYS464 was the most diverse Y-STR."
[source: Forensic value of 14 novel STRs on the human Y chromosome]
"The Y-chromosome short tandem repeat (Y-STR) marker DYS464 was first reported by Redd et al. Forensic Sci. Int. (2002) 130:97-111 and appears to be the most polymorphic Y-STR marker discovered to date."
[source: Forensic Value of the Multi-Copy Y-STR Marker DYS464 by John Butler and Richard Schoske]
"DYS464 is expected to be the most useful marker that can be included in the expanded minimal haplotype."
[source: Forensic evaluation and haplotypes of 19 Y-chromosomal STR loci in Koreans by Myung Jin Park, Hwan Young Lee, Ji-Eun Yoo, Ukhee Chung, Seon Yeong Lee, and Kyoung-Jin Shin]
"The multi-copy loci DYS464, DYS385, and YCAII were the most polymorphic followed by the following single copy Y-STRs: DYS458, DYS390, DYS447, DYS389II, DYS448, and DYS456."
[source: High-throughput Y-STR typing of U.S. populations with 27 regions of the Y chromosome using two multiplex PCR assays by Richard Schoske, Peter M. Vallone, Margaret C. Kline, Janette W. Redman, and John M. Butler]
"DYS 464 is replicated 4 times in 98.5% of people from Europe and the Middle East (the balance having 5 or 6 copies).... In about 1.5% of the test subjects, more than 4 copies will be present, representing Markers 464e, 464f, 464g.... At the current time, 7 copies are the maximum number of Markers found for this DYS."
[source: Family Tree DNA GAP Quick Interpretation Guide]
The Roper DNA site offers and Excel spreadsheet formula to calculate the relative mutations for the DYS464 markers.
Many DYS464 electropherograms are available from DNA-Fingerprint and in the PDF poster on DYS464 by John Butler and Richard Schoske.
This GENEALOGY-DNA mailing list post mentions two other people who got differing DYS464 test results from 2 different labs.
DYF399S1: A Unique Three-Copy Short Tandem Repeat on the Human Y Chromosome, by Gareth Ll. C. Henson, details how DYF399S1 can complement DYS464.
The McGee Surname DNA Project offers a Y-DNA Comparison Utility.
The National Institute of Standards and Technology (NIST) has removed its STR Fact Sheet for DYS464.
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