NIST
Human Identity Team, (L to R) Margaret
Kline, John
Butler, Peter Vallone,
and Amy Decker
JoGG: Briefly, what is NIST and why is it important?
NIST: The National Institute of Standards and
Technology (see http://www.nist.gov)
is a non-regulatory federal agency within the U.S. Department of Commerce. NIST’s mission is to promote U.S. innovation and industrial
competitiveness by advancing measurement science, standards, and technology in
ways that enhance economic security and improve our quality of life. The vision is to be the world’s leader in
creating critical measurement solutions and promoting equitable
standards. With over 3,000 scientists spread primarily over two campuses
in Gaithersburg, Maryland and Boulder, Colorado, NIST efforts center on
stimulating innovation, fostering industrial competitiveness, and improving the
quality of life. NIST aids quality
assurance efforts and helps ensure compatible measurements by generating,
certifying, and issuing Standards Reference Materials (SRMs). NIST defines time for the U.S. (see http://www.time.gov) and produces over 1100
different SRMs to aid measurements in a variety of
fields.
JoGG: Why does NIST have a program in genetics?
NIST: Since the late 1980s, NIST has had scientists
involved in DNA testing. Early concerns over
measurement accuracy and issues with poor quality control of forensic DNA tests caused the Department of
Justice to call upon NIST scientists to help with standards development and
technology evaluation. Through
Congressional funding, the National Institute of Justice (NIJ) has substantially
funded the NIST and other nationwide efforts in improving forensic DNA testing. In 2000 with primary funding from NIJ, a
Human Identity Project Team was established within the Biochemical Science
Division of the Chemical Science and Technology Laboratory (CSTL) at NIST.
As of October 2008, the NIST
Biochemical Science Division has been organized with efforts in Applied
Genetics, DNA Science, Cell Systems Science, Protein Structure and Function,
Bioassay Methods, and Multiplexed Biomolecular Science. There are efforts in our division to improve
measurement capabilities for cell and tissue biological sciences for the
biotech/pharmaceutical industry, DNA damage and repair, and data and
standards applied to the fields of quantitative cell biology, proteomics, gene
expression, and bioinformatics. Because
our Division is tasked with many diverse measurement areas, and considering our
limited staff and resources, we must prioritize our work and look at the impact
in terms of needs for “standardization.” Historically, other agencies, such as the
National Institute of Justice, have funded our work in the area of genetics.
JoGG: What are some of the activities of the Human
Identity Project?
NIST: For the past several years, our Human Identity
Project Team has been part of the DNA Measurements Group of the
Biochemical Science Division. Beginning October
1, 2008,
a new Applied Genetics Group has been formed to focus on forensic, clinical,
and agricultural biotech genetic measurements.
The Applied Genetics Group will continue to produce information,
resources, and reference materials that should be able to benefit the genetic
genealogy community as well although this is not our direct focus.
JoGG: It appears that most of your group’s efforts
go to support the forensics community—is that a fair assessment?
NIST: Yes, our project team is funded through the
National Institute of Justice to conduct research that benefits the human
identity testing community and to create tools that enable forensic DNA laboratories to be more effective
in analyzing DNA. We certify standard reference
materials, conduct interlaboratory studies, produce
new assays to enable improved recovery of information from degraded DNA, evaluate new loci for potential
future use in human identity applications, and generate standard information
and training materials that are made available on the NIST STRBase
website: http://www.cstl.nist.gov/biotech/strbase.
JoGG: There seems to be a
disconnect between the forensics and genetic genealogy communities
concerning the value (usefulness) of Y haplogroups. The forensics community seems to have no
interest in Y haplogroups (why is that?).
Genetic genealogists seem to be completely puzzled as to why forensics
journals publish so many articles on allele frequencies in particular
populations, when those distributions are over mixed haplogroups. On the other hand, allele frequency distributions
within haplogroups are of great interest to genetic genealogists. Surely one or the other of the two
communities is missing something?
NIST: The forensic community is typically focused
on using genetic markers that exhibit the highest possible power of
discrimination. Thus, autosomal DNA testing is preferred over lineage
marker analysis since paternal (in the case of Y chromosome) or maternal (in
the case of mtDNA) relatives would be expected to match. In the case of Y-chromosome testing, Y-STR haplotypes show more variability
than Y-SNP haplogroups. Forensic
analysts are looking for the “biggest bang for their buck,” since they are
usually dealing with low amounts of available sample. Depending on the specific case, it probably
will not be very helpful to know that a sample came from an individual that is
R1b (or even R1b1b2a) because there may be hundreds of people from a region
with potential access to the crime scene that would be considered suspects
based on a Y haplogroup.
Although probably not as
significant of a reason, Y-SNPs haplogroups may also be linked to ethnicity and
thus may be avoided by some labs due to the potential perception of “racial
profiling.” Of course, Y haplogroups have shown their value in human migration
“deep ancestry” studies because they have a much lower mutation rate than Y-STR haplotypes.
Important as well is the fact that
there is no common SNP typing assay platform, core Y-SNP markers, and
widely-accepted commercial kits for Y-SNP analysis. Thus, it would be difficult to prepare reasonable
reference materials or methods.
The bottom line is that each
community is asking different questions.
Forensic labs would like to distinguish suspects who are not the
perpetrator (and have a greater chance that a matching result is to the true
person) while genetic genealogists are looking for matches that link relatives
and thus do not want so much of a genetic separation with their DNA test that they are individualized
and cannot be grouped with related people.
In simple terms, forensic scientists are primarily looking for
exclusions while genealogists are looking for inclusions.
Forensic laboratories, in order to
simplify quality control of their DNA testing reagents, utilize
commercially available kits. Genetic
genealogy test providers on the other hand use proprietary, in-house assays to
analyze many more Y-STR markers than are examined by the forensic community. The currently available Y-STR kits used by forensic DNA labs are PowerPlex
Y (Promega Corporation) and Yfiler
(Applied Biosystems) that examine 12 or 17 Y-STRs,
respectively. Both of these kits examine
a core set of 11 Y-STR loci that were agreed upon in 2003 by a group of
scientists as part of the FBI’s Scientific Working Group on DNA Analysis Methods (SWGDAM).
JoGG: Your group maintains a Y-STR database with 11 markers. Why don’t you determine the haplogroup for
each haplotype? Wouldn’t that help
determine if the haplogroup would have value for the forensics community? Why isn’t this database searchable on all of
the Y-STR data that you have available (many of your samples have
been tested on many more than 11 markers)?
NIST: Actually, Y haplogroups generated with 42
Y-SNPs have been available on a subset of our population samples since July
2004 (Vallone and Butler, 2004). We found only 18 different haplogroups in 229
individuals tested and therefore decided that Y-SNPs were not as useful as
Y-STRs in terms of separating unrelated males from one another. Since that work, our Y-chromosome studies
have been focused almost entirely on Y-STRs.
It is worth noting that a major challenge exists in terms of
standardizing Y haplogroup measurements against a constantly expanding
phylogenetic tree.
More recently our entire set of
samples has been categorized into 19 Y haplogroups (with a set of 19 Y-SNPs)
through collaboration with scientists in the Netherlands.
This data will be forthcoming as part of an effort to understand
ethnicity estimation capabilities and SNP variation across autosomal,
Y-chromosome, and mitochondrial DNA compared to autosomal
STRs and Y-STRs in the same sample set.
There are searchable databases
containing all of our Y-STR data. The 17-locus
Yfiler haplotypes from over 650 NIST samples have
been included as anonymous samples in both the US Y-STR Database (see http://www.usystrdatabase.org/) and
the YHRD database (see http://www.yhrd.org/).
Our U.S. population samples (see http://www.cstl.nist.gov/biotech/strbase/NISTpop.htm)
were obtained as anonymous blood donors from multiple blood banks and thus
cannot be linked to any particular family or individual. The condition of anonymity was required by
our institutional review board at NIST that approves the use of biological
samples. Thus, while these samples are
valuable to study general marker variation, they are less helpful for genetic
genealogical analysis that may be interested in linking a result to a specific
individual or family surname.
It is also worth noting that
studies from various forensic labs around the world have found that
approximately 95% of samples examined can be differentiated from one another
with the 17 Y-STR markers found in the Yfiler kit. So, in terms of forensics investigations,
this is typically enough information especially since these labs are testing
limited amounts of biological evidence and may not have enough material for
more than one or two multiplexed PCR amplifications. However, for research purposes, our
laboratory at NIST and Jack Ballantyne’s lab at the University of Central Florida have examined a number of
additional Y-STR loci to see how well samples can be resolved from one another with
additional haplotype information. Our
groups have developed numerous Y-STR assays, sought to understand
which Y-STR loci are optimal for resolving
paternal lineages, and examined mutation rates in father/son pairs.
JoGG: What are some of the specific activities of
your group that JoGG readers may be interested in?
NIST: The certificate for SRM 2395 Human Y-chromosome DNA Profiling Standard (see http://www.cstl.nist.gov/biotech/strbase/srm2395.htm)
has been updated to include information on new Y-STR loci—again with a primary focus
on markers used in forensics or showing a high degree of variability. We hope to contribute to future discussions
regarding STR nomenclature issues and feel that our certified reference materials
can play a role in aiding quality measurements and reporting by the genetic
genealogy companies. We have also
examined the impact of additional Y-STR markers in terms of resolving
common types (see Decker et al., 2007; and presentations available on our web
site— http://www.cstl.nist.gov/biotech/strbase/NISTpub.htm). A set of almost 400 father-son samples were
examined at the 17 Yfiler loci to measure mutation
rates (Decker et al., 2008).
JoGG: You have a table on your web site with
information on about 80 Y-STR markers. If you count up all of the Y-STR markers offered for testing by
all of the genetic genealogy labs, there are about 120 of them, depending on
just how one counts.
Are these all of the Y-STR markers that are likely to become
available to the genetic genealogy community, or are there significantly more
that could be developed?
NIST: The table you are referring to on our NIST
website is the Y-STR Fact Sheet page (see http://www.cstl.nist.gov/biotech/strbase/ystr_fact.htm). Yes, there are many Y-STR markers that are not yet included
on this page. We intend to continue
adding information to this page as there are over 400 Y-STR markers characterized on the
Y-chromosome. However, many of the loci
formally located on the Y-chromosome have significant homology (sequence
similarity) with the X-chromosome making it very difficult to design a
Y-chromosome-specific assay. In
addition, some information has not been verified or cannot be found in our
searches of available public genomic databases.
Our list of Y-STRs contains 151
markers, considerably fewer than 400, because some are not submitted correctly
(repeated or redundant--different names for the same Y-STR), and some can not be found in
GenBank (not enough information found).
Most of our studies have focused on 82 Y-STRs that we originally thought
might be informative in U.S. populations. However, some of these Y-STRs only had one or
two alleles at that locus, which does not help in discriminating between
individuals. What we have done has been
fairly comprehensive in terms of reviewing Y-STR loci; therefore, we probably
won’t come across a “new” set of loci
that are better than what is already being used.
JoGG: How much of the Y chromosome has been
searched for Y-STRs?
NIST: More than half of the human Y-chromosome has
never been sequenced—and probably never will be. The Human Genome Project did not attempt to
determine the complex repeat patterns found on the long arm of the Y-chromosome
in what is commonly referred to as the “heterochromatic region.” The remaining euchromatic region, which is approximately 23 million bases
in length, was reported as the “finished” reference Y-chromosome published in
the June 19, 2003 issue of Nature by
researchers from the Whitehead Institute and Washington University.
About five years ago, Manfred Kayser, a German scientist now at Erasmus University in Rotterdam (the Netherlands), led a group in comprehensively
characterizing Y-STR markers. Their
efforts were published in the June 2004 issue of the American Journal of
Human Genetics (Kayser, 2004). Kayser’s team found
166 new Y-STRs of which 139 were polymorphic in a set of eight diverse
samples.
Erin Hanson and Jack Ballantyne from the University of Central Florida published an article in the March
2006 issue of the journal Legal Medicine which describes at least 417
separate Y-STR markers based on information deposited in public databases. The figures and tables from their article are
available at http://ncfs.ucf.edu/ystar/ystar.html. As they note in their Table 2 there are, unfortunately,
many redundant Y-STR locus designations meaning that the true number of “real”
Y-STRs is less than 400.
It is important to realize that
not all Y-STR markers are of equal value in terms of exhibiting variation between
individuals or being able to be PCR-amplified as Y-chromosome
specific. In order to examine variation
in individual samples, Y-STR markers must also be put into multiplex assays that work
reliably to order to make sample testing more manageable and cost
effective. Thus, not every Y-STR marker that exists on the human
Y-chromosome is going to be useful or used.
JoGG: There are now about one million SNPs tested
simultaneously by “gene chips” such as the Illumina
chip. How likely is it that someone will
develop a chip that could measure hundreds (or thousands?) of Y-STRs at once?
NIST: The Illumina SNP
chip systems, such as used by 23andMe, can generate an incredible amount of
genetic information from bi-allelic SNP markers. Unfortunately, these hybridization arrays are
unable to analyze multi-allelic STR markers. Thus, Y-STRs will continue to be processed
for the foreseeable future with proven capillary electrophoresis technology.
JoGG: Your web site now has some references to
genetic genealogy. What role would you like
NIST to play in the genetic genealogy area?
NIST: While our focus has been on Y-STR markers of forensic interest due
to funding in this area, we certainly would like to see measurements performed properly
and consistently between genetic genealogy test providers. Hopefully our efforts in producing the Human
Y-chromosome DNA Profiling Standard Reference Material (SRM 2395) – see
http://www.cstl.nist.gov/biotech/strbase/srm2395.htm
will aid genetic
genealogy as well as forensic DNA Y-chromosome
analysis. Unfortunately, we probably will not be able
to easily provide certified reference values for all Y-STR loci currently under examination
by the genetic genealogy community due to limited resources at NIST. We have reviewed information on specific Y-STR loci per requests in the past,
made nomenclature recommendations, and provided genetic diversity information
on a number of Y-STR markers.
JoGG: One of the biggest problems in the genetic
genealogy community is the different Y-STR nomenclature standards used by
different labs. FTDNA stated at its last
meeting in Houston that they had written to you and
requested that NIST provide guidance on how each marker should be scored. Have you responded to this request? Can we expect NIST to make public some
recommendations in this area, and when might that happen?
NIST: In October 2007, at the International
Symposium on Human Identification, John Butler met with Matt Kaplan, Taylor
Edwards, and Thomas Krahn from FamilyTree DNA and discussed a number of
specific Y-STR nomenclature examples.
The DNA Commission of the International
Society of Forensic Genetics (ISFG), in their latest update of recommendations
on the use of Y-STRs in forensic analysis, has published eight nomenclature
guidelines (Gusmão et al., 2006). Specific guidance is given on over 70 Y-STRs
(see their Tables 1 and 2). However,
there are some additional Y-STRs run by progressive genetic genealogy companies
that are not included in this article.
Unfortunately, these recommendations do not necessarily capture all
possibilities and some ambiguity can exist, especially with more complex repeat
structures.
The five male sample components
present in the NIST SRM 2395 Human Y-chromosome DNA Profiling reference material have
been certified for some additional Y-STRs.
We have prepared a paper (Butler, et al., 2008--see this issue of
JoGG) to address some of the issues seen with Y-STRs we have reviewed in our
lab and included on the SRM 2395 update.
JoGG: If a genetic genealogy company decides to
introduce a new marker, would your group be willing to provide advice on
scoring it?
NIST: We are open to discussing new loci, our
response to whether or not we can assist in determining repeat motifs will
depend on our focus at the time of the request. We will try to assist as time
and resources permit. Knowledge of what loci are being investigated assist us
in assessing standards needs that help formulate our future plans
JoGG: What can the genetic genealogy community do
for your group?
NIST: Please continue to inform us about what
information is of interest to the genetic genealogy community (such as
consistent nomenclature with Y-STRs) and continue open communication with us on
ideas and projects. Realize that our
focus is where our funding is and therefore we cannot always respond to every
desire of those who contact us. Although
we are spread thin and working on other projects, we definitely would like to
support progress and quality measurements in genetic genealogy.
Web Resources
http://www.usystrdatabase.org/
U. S. Y-STR Database
http://www.yhrd.org/
International
YHRD Database
http://www.cstl.nist.gov/biotech/strbase/srm2395.htm
SRM 2395 Human Y-Chromosome Profiling
Standard
References
Butler, J.M., Kline, M.C.,
Decker, A.E. (2008) Addressing
Y-chromosome short tandem repeat (Y-STR) allele nomenclature. J Genet Geneal,
4:125-148.
Decker
AE, Kline MC, Redman JW, Reid TM, Butler JM (2008) Analysis of mutations in father-son pairs with
17 Y-STR loci. FSI Genetics,
2(3):e31-e35.
Gusmão L, Butler JM, Carracedo A,
Gill P, Kayser M, Mayr WR, Morling N, Prinz M, Roewer L, Tyler-Smith C, Schneider PM (2006) DNA Commission of the International Society
of Forensic Genetics (ISFG): an update of the recommendations on the use of
Y-STRs in forensic analysis. Forensic
Sci Int, 157:187-197.
Hanson
EK, Ballantyne J (2006) Comprehensive
annotated STR physical map of the human Y chromosome: forensic
implications. Legal Med,
8:110-120; see also http://ncfs.ucf.edu/ystar/ystar.html
Kayser M, Kittler R, Ralf A, Hedman
M, Lee AC, Mohyuddin A, Mehdi SQ, Rosser Z, Stoneking M, Jobling MA, Sajantila
A, Tyler-Smith C (2004) A comprehensive
survey of human Y-chromosomal microsatellites.
Am J Hum Genet, 74(6):1183-1197.
Skaletsky H, Kuroda-Kawaguchi T, Minx PJ, Cordum HS, Hillier L, Brown LG, Repping
S, Pyntikova T, Ali J, Bieri
T, Chinwalla A, Delehaunty
A, Delehaunty K, Du H, Fewell G, Fulton L, Fulton R, Graves T, Hou
SF, Latrielle P, Leonard S, Mardis
E, Maupin R, McPherson J, Miner T, Nash W, Nguyen C, Ozersky
P, Pepin K, Rock S, Rohlfing T, Scott K, Schultz B,
Strong C, Tin-Wollam A, Yang SP, Waterston RH, Wilson
RK, Rozen S, Page DC (2003) The male-specific region of the human Y
chromosome is a mosaic of discrete sequence classes. Nature, 453:825-837.
Vallone P, Butler J (2004)
Y-SNP typing of U.S. African American and Caucasian samples using
allele-specific hybridization and primer extension. J Forensic Sci, 49(4):723-732.