Biology:List of Y-STR markers
The Y-STR markers in the following list are commonly used in forensic[1] and genealogical DNA testing.
DYS454 is the least diverse, and multi-copy marker DYS464 is the most diverse Y-STR marker.
The location on the Y-chromosome of numbered Y-STR markers can be roughly given with cytogenetic localization. For example, DYS449 is located at Yp11.2 - meaning the Y-chromosome, petit arm, band 1, sub-band 1, sub-sub-band 2 - DYS449.[2]
Forensic labs usually use PowerPlex Y (Promega Corporation) and Yfiler (Applied Biosystems) kits that examine 12 or 17 Y-STRs, respectively. Genealogical DNA test labs examine up to 700 Y-STRs.
Mutation rates
Mutation rates are those per generation, as estimated in Chandler (2006).[3] The quoted estimated errors are typically +/- 15-20%. Alternative estimates (for forensic use therefore not all markers are covered) from observed pedigrees are also available at the Y Chromosome Haplotype Reference Database.
It appears that some trinucleotide markers may have much higher mutation rates at some repeat lengths than at others. For example, variation of the trinucleotide DYS388 is generally very slow in most haplogroups, when it takes the values 11–13. But there appears to be much greater variation and more rapid mutation in Haplogroup J, where it typically has values 14–18. Similarly the trinucleotide DYS392 is reported to be "fast" in haplogroups N and Q, where it takes values 14-16 which are rare in other groups.[4]
Y-STR markers
| STR | Notes | DNA sequence repeat motif | Alleles | Mutation rate | Links |
|---|---|---|---|---|---|
| DYS19=14 | see DYS394 | — | — | — | — |
| DYS385 | DYS385 is a multi-copy marker, and includes DYS385a and DYS385b. The order of DYS385a and DYS385b may be reversed, their sequence is referred to as the Kittler order. | GAAA | 13-18 | 0.00226 | NIST fact sheet |
| DYS388 | ATT | 17 | 0.00022 [5] | ||
| DYS389 | DYS389 is a multi-copy marker, and includes DYS389i and DYS389ii. DYS389ii refers to the total length of DYS389. Therefore, when there is a one step mutation at DYS389i, it will also appear in DYS389ii. | (TCTG) (TCTA) (TCTG) (TCTA) | i:13 ii:30 |
0.00186, 0.00242 | NIST fact sheet |
| DYS390 | (TCTA) (TCTG) | 23 | 0.00311 | NIST fact sheet | |
| DYS391 | TCTA | 11 | 0.00265 | NIST fact sheet | |
| DYS392 | TAT | 11 | 0.00052 [5] | NIST fact sheet | |
| DYS393 | DYS393 is also known as DYS395. | AGAT | 12 | 0.00076 | NIST fact sheet |
| DYS394 | DYS394 is also known as DYS19. | TAGA | 14 | 0.00151 | NIST fact sheet |
| DYS413 | Found in the Palindromic region of the Y DNA | 21-22 | |||
| DYS425 | DYS425, when it can be measured, is very stable. However it is actually one copy of a multiple part marker, DYF371 (below), and as such recLOH mutations can often make it unmeasurable when the other copies overwrite it. For example, it is associated with the defining SNP for I-M38 (I2a2a1a1; formerly I1b2a1), as the SNP M284 can render a null value at this marker. Most members of E-M96 and sub-clades also render null values. Nevertheless, it was one of the small number of markers originally offered by Oxford Ancestors, and Family Tree DNA later chose to offer it to genealogists also. | TGT | 12 | [5] | |
| DYS426 | GTT | 11 | 0.00009 [5] | NIST fact sheet | |
| DYS434 | TAAT (CTAT) | 9 | NIST fact sheet | ||
| DYS435 | TGGA 11 |
||||
| DYS436 | GTT | 12 | [5] | ||
| DYS437 | TCTA | 14 | 0.00099 | NIST fact sheet | |
| DYS438 | TTTTC | 10 | 0.00055 | NIST fact sheet | |
| DYS439 | DYS439 is also known as Y-GATA-A4. DYS439 is associated with the defining SNP for haplogroup R1b1c9a, as the SNP can render a null value at this marker. | AGAT | 12 | 0.00477 | NIST fact sheet |
| DYS441 | CCTT | 15 | A novel multiplex PCR system | ||
| DYS442 | TATC | 11 | 0.00324 | A novel multiplex PCR system | |
| DYS443 | TTCC 0 |
||||
| DYS444 | TAGA | 11 | A novel multiplex PCR system | ||
| DYS445 | TTTA | 11 | A novel multiplex PCR system | ||
| DYS446 | TCTCT | 14 | Sorenson Marker Details | ||
| DYS447 | TAAWA | 26 | 0.00264 | NIST fact sheet | |
| DYS448 | AGAGAT | 20 | 0.00135 | NIST fact sheet | |
| DYS449 | TTTC | 25 | 0.00838 | Sorenson Marker Details | |
| DYS450 | TTTTA | 8 | |||
| DYS452 | YATAC | 29 | |||
| DYS453 | AAAT | 0 | |||
DYS454
|
DYS454 is the least varying Y-STR marker commonly used in genealogical DNA testing. Of the entries for DYS454 at Ybase, 96% have 11 repeats, 3% have 10 repeats, and 2% have 12 repeats (source). | AAAT | 11 | 0.00016 | |
| DYS455 | AAAT | 11 | 0.00016 | Sorenson Marker Details | |
| DYS456 | AGAT | 14 | 0.00735 | Sorenson Marker Details | |
| DYS458 | GAAA | 18 | 0.00814 | Sorenson Marker Details | |
| DYS459 | This is a multi-copy marker, and includes DYS459a and DYS459b. | TAAA | 8-9 | 0.00132 | |
| DYS460 | DYS460 was originally known as Y-GATA-A7.1. | ATAG | 10 | 0.00402 | NIST fact sheet |
| DYS461 | DYS461 was originally known as Y-GATA-A7.2. | (TAGA) CAGA | 11 | NIST fact sheet | |
| DYS462 | TATG | 11 | |||
| DYS463 | AARGG | 22 | |||
DYS464
|
DYS464 is a multi-copy palindromic marker. Men typically have four copies known in such cases as DYS464a, DYS464b, DYS464c, and DYS464d. There can be less than four copies, or more, which in such cases would be known as DYS464e, DYS464f, etc. DYS464 is the most diverse range of values of any Y-STR marker (source). This marker can also sometimes be typed with separate g-types and c-types to increase resolution. The type variance is based on a SNP that can be found in most R1b haplogroup males. It is part of the Palindromic region of Y DNA | CCTT | 12-14-16-17 | 0.00566 | Forensic value of the multicopy Y-STR marker DYS464 |
| DYS481 | CTT | 26 | [5] | ||
| DYS485 | TTA | 15 | [5] | ||
| DYS487 | ATT | 13 | [5] | ||
| DYS490 | TTA | 12 | [5] | ||
| DYS494 | TAT | 9 | [5] | ||
| DYS495 | AAT | 15 | [5] | ||
| DYS497 | TAT | 15 | [5] | ||
| DYS504 | 14 | ||||
| DYS505 | TCCT | 13 | |||
| DYS508 | TATC | 0 | |||
| DYS518 | AAAG | 0 | NIST Comm. Kits | ||
| DYS520 | ATAS | 21 | |||
| DYS522 | GATA | 13 | |||
| DYS525 | TAGA | 10 | |||
| DYS531 | AAAT | 11 | |||
| DYS532 | CTTT | 10 | |||
| DYS533 | ATCT | 11 | |||
| DYS534 | CTTT | 15 | |||
| DYS540 | TTAT | 11 | |||
| DYS549 | AGAT | 13 | |||
| DYS556 | AATA | 12 | |||
| DYS557 | TTTC | 18 | |||
| DYS565 | TAAA | 11 | |||
| DYS570 | TTTC | 12-23 | 0.00790 | ||
| DYS572 | AAAT | 12 | |||
| DYS573 | TTTA | 0 | |||
| DYS575 | AAAT | 8-12 | |||
| DYS576 | AAAG | 17 | 0.01022 | ||
| DYS578 | AAAT | 8 | |||
| DYS589 | TTATT | 11 | |||
| DYS590 | TTTTG | 8 | |||
| DYS594 | TAAAA | 10 | |||
| DYS607 | AAGG | 14 | 0.00411 | ||
| DYS612 | |||||
| DYS614 | |||||
| DYS626 | AAAG | ||||
| DYS627 | AAAG | 0 | NIST Comm. Kits | ||
| DYS632 | CATT | 8 | |||
| DYS635 | Also known as Y-GATA-C4 | TSTA compound | 21 | 0.0046 | NIST fact sheet |
| DYS636 | 11 | ||||
| DYS638 | TTTA | 11 | |||
| DYS641 | TAAA | 10 | |||
| DYS643 | CTTTT | 9 | |||
| DYS710 | GAAA | 36 | |||
| DYS714 | TTTTC | 25 | |||
| DYS716 | CCATT | 27 | |||
| DYS717 | TGTAT | 20 | |||
| DYS724 | Palindromic; also known as CDY | 33-35 | 0.03531 | ||
| DYS725 | Palindromic | ||||
| DYS726 | YSTR marker in the pericentromeric region. | 12 | |||
| DYF371 | DYF371 is a multicopy, palindromic region marker. Includes the DYS425 marker & can be informative in cases of null values at that marker. | 12 | |||
| DYF385S1 | Duplicated YSTR marker in close proximity to DYS459 | 8-9 | |||
| DYF387S1 a/b | RAAG | 0 | NIST Comm. Kits | ||
| DYF397 | DYF397 is a palindromic region marker. | ||||
DYF399
|
An asymmetric three allele STR locus that can be used to observe deletions and recombinational rearrangements in the palindromic region of the Y chromosome. | 17-29 (many incomplete alleles) | nomenclature | ||
| DYF401 | DYF401 is a palindromic region marker. | ||||
| DYF406S1 | 11 | ||||
| DYF408 | DYF408 is a palindromic region marker. | ||||
| DYF411 | DYF411 is a palindromic region marker. | ||||
| DXYS156 | |||||
| YCAII | YCAII is a multi-copy marker which includes YCAIIa & YCAIIb | 22-22 | 0.00123 | ||
| Y-GATA-H4 | TAGA | 10 | 0.00208 | NIST fact sheet | |
| Y-GATA-C4 | see DYS635 | ||||
| Y-GATA-A10 | TAGA | 14 | NIST fact sheet | ||
| Y-GGAAT-1B07 | 11 |
Y-STR allele nomenclatures
DNA testing companies or labs in certain cases use different nomenclatures to designate the same Y-STR allele. Thus, a conversion must be applied in these cases to accurately compare Y-STR results obtained from different companies. The most common nomenclature is based on guidance provided by NIST for Y-STR markers historically reported differently by various companies. The NIST standard is the proposal of ISOGG (International Society of Genetic Genealogy) for genetic genealogy companies.[6][7]
Notes and references
- ↑ "Interview with John Butler and Members of the NIST Human Identity Project Team". JoGG. http://www.jogg.info/42/files/Interview.htm. Retrieved 11 August 2012.
- ↑ DYS449 in the GDB Human Genome Database
- ↑ Chandler (2006) (but see also this mailing list discussion)
- ↑ "GENEALOGY-DNA-L Archives — DYS 388 Mutation Rate?". http://archiver.rootsweb.com/th/read/GENEALOGY-DNA/2004-10/1098899485.
- ↑ 5.00 5.01 5.02 5.03 5.04 5.05 5.06 5.07 5.08 5.09 5.10 5.11 Trinucleotide - see #Mutation rates
- ↑ "Marker Standards". Sorenson Molecular Genealogy Foundation. http://www.smgf.org/ychromosome/marker_standards.jspx. Retrieved 11 August 2012.
- ↑ Matthiesen, Diana Gale (19 July 2011). "Converting Y-DNA STR Test Results between SMGF, AncestryDNA, and FamilyTreeDNA". http://dgmweb.net/DNA/General/ADNA_FTDNA.html. Retrieved 11 August 2012.
- Kayser et al. (2004), A Comprehensive Survey of Human Y-Chromosomal Microsatellites Am. J. Hum. Genet., 74 1183–1197. NB online only data file
- Krahn, Thomas. "Y-STR fingerprint - Panels". Price List DNA-Fingerprint - Genealogy Testing Services. http://www.dna-fingerprint.com/static/pricelist.pdf. Retrieved 11 August 2012.
- Butler, John M. (9 January 2012). "Y-Chromosome STRs". Short Tandem Repeat DNA. NIST Standard Reference Database SRD 130. http://www.cstl.nist.gov/biotech/strbase/y_strs.htm. Retrieved 11 August 2012.
- Butler, John; Kline, Decker (2009-06-29). "Summary List of Y Chromosome STR Loci and Available Fact Sheets". NIST Standard Reference Database SRD 130. http://www.cstl.nist.gov/biotech/strbase/ystr_fact.htm. Retrieved 11 August 2012.
See also
External links
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