MARKER & MUTATION COMPARISON

Reprinted with permission of John Chandler.  Copied from the Genealogy-DNA-List archives.


John Chandler's posting from September 2005 at Genealogy-DNA-L

Time for another update on mutation rates. I downloaded 2122 37-marker haplotypes from Ysearch, representing a mix of haplogroups, and used the method described in the SMGF poster ASHG 2004-4, entitled "Direct determination of mutation characteristics of Y chromosome STR loci," to determine the mutation rates. However, I used the recently augmented YHRD table of direct mutation-rate measurements from father-son pairs as the calibration. I also converted the reported SMGF rates to the same new calibration scale for comparison. Finally, I computed the average rates for a variety of panels and tossed in the corresponding panel averages announced by FTDNA at last year's conference and the ones calculated from Charles Kerchner's log as of now. Note: the multi-copy markers are shown here with the rate for each copy assuming equipartition, and the panel averages are computed by counting each copy as a separate marker.  Note the peculiarity of the log data: the average for 1-25 is higher than either 1-12 or 13-25. This suggests a bias in the decisions to upgrade from 12 to 25 -- those with observed mutations in a 12-marker test were significantly more likely to upgrade than those with a 12/12 match. In particular, the average rate for the 12-marker tests of those who upgraded is 0.00267, while the average for those who did not upgrade is 0.00175.

Locus ____ --SMGF_ASHG_2004-4---

_______ YSEARCH ____ FTDNA ____ K_Log

_____ ____ (poster) ____ (scale) ____ (scale)

385ab ____ 0.002800 ____ 0.00230 ____ 0.00217

388 ______ 0.000379 ____ 0.00031 ____ 0.00040

389i _____ 0.002184 ____ 0.00179 ____ 0.00179

389ii-i ____ 0.002584 ____ 0.00212 ____ 0.00219

390 ______ 0.004405 ____ 0.00361 ____ 0.00370

391 ______ 0.003155 ____ 0.00259 ____ 0.00255

392 ______ 0.001488 ____ 0.00122 ____ 0.00136

393 ______ 0.001119 ____ 0.00092 ____ 0.00090

394 ______ 0.001548 ____ 0.00127 ____ 0.00123

426 ______ 0.000271 ____ 0.00022 ____ 0.00024

437 ______ 0.001755 ____ 0.00144 ____ 0.00144

438 ______ 0.001018 ____ 0.00084 ____ 0.00077

439 ______ 0.004181 ____ 0.00343 ____ 0.00349

441 ______ 0.001323 ____ 0.00109 ____ -------

442 ______ 0.003066 ____ 0.00252 ____ 0.00232

444 ______ 0.002956 ____ 0.00243 ____ -------

445 ______ 0.000952 ____ 0.00078 ____ -------

446 ______ 0.003143 ____ 0.00258 ____ -------

447 ______ 0.003891 ____ 0.00319 ____ 0.00308

448 ______ 0.002375 ____ 0.00195 ____ 0.00202

449 ______ 0.006464 ____ 0.00531 ____ 0.00574

452 ______ 0.001743 ____ 0.00143 ____ -------

454 ______ 0.000235 ____ 0.00019 ____ 0.00024

455 ______ 0.000312 ____ 0.00026 ____ 0.00032

456 ______ 0.005342 ____ 0.00439 ____ 0.00470

458 ______ 0.005804 ____ 0.00476 ____ 0.00484

459ab ____ 0.001176 ____ 0.00097 ____ 0.00091

460 ______ 0.002942 ____ 0.00241 ____ 0.00241

461 ______ 0.002327 ____ 0.00191 ____ -------

462 ______ 0.000532 ____ 0.00044 ____ -------

463 ______ 0.001623 ____ 0.00133 ____ -------

464abcd __ ------ * ____ ---- ** ____ 0.00279

570 ______ -------- ____ ------- ____ 0.00447

576 ______ -------- ____ ------- ____ 0.00549

607 ______ -------- ____ ------- ____ 0.00309

A10 ______ 0.003794 ____ 0.00311 ____ -------

C4 _______ 0.002355 ____ 0.00193 ____ -------

H4 _______ 0.003044 ____ 0.00250 ____ 0.00259

YCAIIab __ 0.001249 ____ 0.00102 ____ 0.00108

1B07 _____ 0.000925 ____ 0.00076 ____ -------

CDYab ____ -------- ____ ------- ____ 0.00672

Panels:

FT1-12 ___ 0.002242 ____ 0.00184 ____ 0.00185 ____ 0.00399 ___ 0.00245

FT13-25 __ 0.002860 ____ 0.00235 ____ 0.00236 ____ 0.00481 ___ 0.00256

FT1-25 ___ 0.002560 ____ 0.00210 ____ 0.00211 ____ 0.00441 ___ 0.00261

FT1-37 ___ ------------- ____ ------------ ____ 0.00255 ____ 0.00541 ___ 0.00450

RG26 _____ 0.002020 ____ 0.00166 ____ -------

RG43 _____ 0.002410 ____ 0.00198 ____ -------

Norway10__ 0.002245 ____ 0.00184 ____ 0.00185 ***

YHRD10 ___ 0.002530 ____ 0.00208 ____ 0.00208 ****

* Used 0.00350 for calculating panel averages.

** Used 0.00287 for calculating panel averages.

*** Panel of ten markers used in Norwegian father-son study, with a measured average rate of 0.0020. (Dupuy et al. 2004).

**** Panel of ten markers with collected published (or almost published) results, including the Norwegion study, but not the same ten markers.


 


 

Date: Tue, 12 Apr 2005 21:37:24 -0400 (EDT)
From: John Chandler
To: GENEALOGY-DNA-L@rootsweb.com

Subject: STR mutation rates again

With the new release of data and software at the SMGF software, it's
time to take another look at the mutation rates.  The old version of
smgf.org had a peculiar kink in the probability curve for a perfect
match, such that the stated probability was always a little low for
the submitter and always a little high for everyone else.  That kink
is gone now.  More importantly, there are eight loci there now that
weren't there before.  I have read off the implied mutation rates from
the web site, using a simple and robust method.  Note: the MRCA
likelihoods are reported there to 8 decimal digits, but I am including
only 5 decimal digits in the derived mutation rates here.  The
absolute calibration is still not published.

Here's the "executive summary".

- The table of rates deduced from SMGF by Doug McDonald using a less
reliable method and reported last year, and now displayed with some
updates on the World Families Network web site, is noticeably higher
than the rates assumed at SMGF, by about 10% on average.

- All of the 28 markers displayed at SMGF last year still have exactly
the same rate estimates, to within one or two at the 8th decimal digit.

- The 8 "new" markers, alas, do not have locus-specific rates in this
release of the web site.  All 8 have an identical assumed rate of
0.002.

In the table below, I show the implicit SMGF mutation rates and, for
comparison, the rates listed at WFN.  The multi-copy marker rates here
are per-copy.

I also show the averages for various panels of markers (using Doug's
estimate of 0.0035 for DYS464 as needed.)

Locus ____ -SMGF-- ___ -WFN--
385ab ____ 0.00280 ___ 0.0033
388 ______ 0.00038 ___ 0.0005 *
389i _____ 0.00218 ___ 0.0021
389ii-i __ 0.00257 ___ 0.0028
390 ______ 0.00440 ___ 0.0045
391 ______ 0.00316 ___ 0.0036
392 ______ 0.00147 ___ 0.0016
393 ______ 0.00111 ___ 0.0012
394 ______ 0.00153 ___ 0.0016
426 ______ 0.00027 ___ 0.0005
437 ______ 0.00174 ___ 0.0020
438 ______ 0.00100 ___ 0.0012
439 ______ 0.00418 ___ 0.0045
441 ______ 0.00200** _ ------
442 ______ 0.00200** _ ------
444 ______ 0.00200** _ ------
445 ______ 0.00200** _ ------
446 ______ 0.00200** _ ------
447 ______ 0.00388 ___ 0.0045
448 ______ 0.00236 ___ 0.0028
449 ______ 0.00646 ___ 0.0075
452 ______ 0.00200** _ ------
454 ______ 0.00023 ___ 0.0005
455 ______ 0.00031 ___ 0.0005
456 ______ 0.00200** _ ------
458 ______ 0.00580 ___ 0.0066
459ab ____ 0.00118 ___ 0.0014
460 ______ 0.00294 ___ 0.0028
461 ______ 0.00231 ___ 0.0028
462 ______ 0.00053 ___ 0.0005
463 ______ 0.00200** _ ------
464abcd __ ------- ___ 0.0035
A10 ______ 0.00380 ___ 0.0045
C4 _______ 0.00236 ___ 0.0028
H4 _______ 0.00304 ___ 0.0036
YCAIIab __ 0.00124 ___ 0.0014
1B07 _____ 0.00091 ___ 0.0013

 panels:
FT1-12 ___ 0.00224 ___ 0.00246
FT13-25 __ 0.00286 ___ 0.00317
FT1-25 ___ 0.00256 ___ 0.00283
RG26 _____ 0.00202 ___ 0.00228
RG43 _____ 0.00231 ___ 0.00253
Norway10__ 0.00224   ***

* Also listed as 0.0006 in the Relative Genetics Panel.
** An obviously arbitrary figure.
*** Panel of ten markers used in Norwegian father-son study, with a
measured average rate of 0.0020. (Dupuy et al. 2004).


A few words on the method of reading these rates from the web site:

For an exact match, neglecting the possibility of mutations that
cancel each other out, the likelihood is proportional to the 2N'th
power of the probability that all markers fail to mutate in a
transmission event.  Thus, it is only necessary to pull out the ratio
of likelihoods between generations for two cases: one where all
markers are verified to match and another where one marker is ignored.
The ratio between these two ratios is the square of the probability
that the selected marker did not mutate.  I have verified that the
ratios from generation to generation are all the same in the SMGF
calculation (now that the "kink" is gone), thus demonstrating that
their calculation does indeed neglect the possibility of cancellation.
Even with the kink in place last year, all ratios except the first
were the same.

					John Chandler
Note: the rates that John Chandler mentions for "WFN" are found at this page:  http://www.worldfamilies.net/marker