SWGDAM Y-STR Interpretation Guidelines

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QUESTION:  Our laboratory utilizes a direct-to-DNA approach for the analysis of Sexual Assault Forensic Evidence (SAFE) Kits, where qPCR is used to screen samples for the presence of male DNA (Y-screen).  We have dedicated personnel who extract and perform qPCR on evidence samples from these kits, interpret the results of the qPCR, and issue a report containing the results of the Y-screen.  These individuals do not perform any other aspect of DNA analysis.  After the completion of the Y-screen workflow, either the SAFE kit swabs or the already-prepared extracts are forwarded to a separate section of the laboratory for autosomal or Y-STR analysis, as appropriate.  Are the individuals performing the Y-screen workflow subject to the DNA analyst requirements of the QAS?

SWGDAM Response: Yes.  Individuals who interpret Y-screen results and/or prepare reports are considered analysts under the QAS and are bound by all applicable requirements, including but not limited to those requirements related to education, training, experience, and proficiency testing.  In this scenario, individuals who extract and perform qPCR, but do not interpret the Y-screen results or prepare reports, are considered technicians under the QAS.

QUESTION:  What if the Y-screen extracts are discarded after qPCR and are never used for STR analysis? 

SWGDAM Response:  Even if the extracts are discarded after performing the Y-screen, the individual interpreting the qPCR results and/or preparing a report is considered an analyst and subject to the QAS requirements as described above. 

SWGDAM recognizes the need for further clarification on the application of the Quality Assurance Standards to Y-screening workflows and a SWGDAM Communication is currently in progress.  In the interim, proficiency testing requirements related to qPCR workflows can be found in the SWGDAM Clarification on Proficiency Testing of qPCR Workflows Including Y-screening. 

QUESTION: I am hoping you can shed light on YFiler Plus…regarding the update of the statistical calculations for the US Y-STR database. Prior communication…indicates that there [is] insufficient YFiler Plus data available to perform empirical theta calculations. Based on the current data available, can the statistical calculation be updated for YFiler Plus?

SWGDAM Response:  The SWGDAM Interpretation Guidelines for Y-Chromosome STR Typing by Forensic DNA Laboratories -Approved 01/09/14 recognize that population substructure exists for Y-STR haplotypes and describes the generation of match probabilities using the haplotype analog of the formulae described in National Research Council (1996) Recommendation 4.2 which incorporates a theta (θ) correction (Section 10.3).  In Appendix 1 of these guidelines, SWGDAM provides estimations of theta (θ) using African American, Asian, Caucasian, Hispanic, and Native American population data from the U.S. Y-STR Database release 3.2 as well as references to other published estimates of theta (θ)  (Section 10.3.3) and acknowledges that the advent of new multiplexes (i.e., with additional-STR loci, or with a different set or subset of loci) may necessitate additional studies of theta (θ) as sufficient haplotype data becomes available for the new multiplex (Section 10.3.4).  The US Y-STR Database Release 4.2 (USYSTR Database) contains 2094 YFiler Plus haplotypes and has been tested by SWGDAM to estimate new theta (θ) values.  Based on its evaluation of these estimates, SWGDAM has chosen to re-evaluate these estimates should a larger sample size of YFiler Plus haplotypes be made available in a future release of the database.  SWGDAM continues to encourage laboratories to consider collaborating with the USYSTR Database to share their Y-STR haplotypes to augment the size of its datasets to increase both the genetic information and discrimination potential of this critical forensic resource.

Until YFiler Plus-specific θ estimates are available, USYSTR Database users who submit a 27-locus YFiler Plus haplotype can still obtain a count of the number of times the haplotype has been observed in the database, its relative frequency and the variation in this estimate based upon database size.  While the USYSTR Database does not presently calculate the theta-dependent match probability, due to the absence of estimates of theta (θ) values for this set of loci, should a YFiler Plus user wish to obtain a match probability estimate, he/she could re-submit the haplotype to the USYSTR Database omitting the YFiler Plus loci DYS449, DYS460, DYS518, DYS627, and DYF387S1. The resulting match probability would be conservative in that, necessarily, it doesn’t take into account the variation at the loci not submitted.

Partial Matching and Familial Searching

Q: There are different recommendations on your website for partial matching and familial searching.  Which is the most recent?                                                                                        

SWGDAM Response: Partial matches are different from familial searching.  A detailed description and explanation of the differences between partial matches and familial searching are available on the Federal Bureau of Investigation’s (FBI) CODIS website (https://www.fbi.gov/services/laboratory/biometric-analysis/codis). SWGDAM has reviewed issues relating to partial matches and familial searching and issued recommendations on each.  In 2009, SWGDAM issued recommendations that were developed in response to a specific request relating to the population genetics and statistics issues for partial matches that occur fortuitously during searches of the National DNA Index System (NDIS).  These recommendations were considered by the FBI in adoption of the plan for the release of information in the event of a partial match at NDIS (contained within the NDIS Operational Procedures Manual, Appendix G; available at https://www.fbi.gov/file-repository/ndis-procedures-manual-ver4-approved-04272016.pdf/view).  For laboratories considering the implementation of familial searching in their jurisdictions, a SWGDAM Ad Hoc Working Group provided guidance in 2013 on several specific questions posed by the FBI’s CODIS Unit  (see Recommendations from the SWGDAM Ad Hoc Working Group on Familial Searching; available at http://media.wix.com/ugd/4344b0_46b5263cab994f16aeedb01419f964f6.pdf).

National Commission on Forensic Science

QUESTION: What plans exist to transition SWGDAM from its current home in the FBI to the new Organization of Scientific Are Committees (OSAC)?
 

SWGDAM Response: Due to the unique statutory relationship between SWGDAM and the FBI with regard to the FBI Director’s Quality Assurance Standards (QAS) for DNA Laboratories, NIST and the FBI have agreed that SWGDAM will remain operationally with the FBI at this time.  The FBI also feels strongly that the business activities of the SWGDAM Committees are critical for the operation of CODIS and plans to continue managing the SWGDAM Committees to ensure not only that the QAS are revised in an efficient manner, but also that the National DNA Index System (NDIS) Procedures are timely and appropriate for the current or emerging technologies which are used by NDIS-participating laboratories nationwide.  Emerging forensic technologies such as Rapid-DNA testing and Next Generation Sequencing (NGS) are quickly becoming a reality, so the FBI must also ensure through SWGDAM that topics such as nomenclature and genetic privacy can be made fully compatible with the CODIS system.  Once the OSAC has disseminated guidance for the review and approval of standards and guidelines through its Forensic Science Code of Practice, draft SWGDAM guideline documents will be submitted for review and comment to the OSAC administration and all approved SWGDAM guidelines will be provided to the OSAC for inclusion in its Registry of Approved Standards or Guidelines, as appropriate.  Additionally, once the OSAC business structure has been formally memorialized, SWGDAM will review its current business process for drafting and approving guidelines which are captured in its Bylaws, and, to the extent possible, incorporate all elements of the review process designated for the OSACs.  This includes a public review period for all guidelines and proposed changes to the QAS which SWGDAM has now implemented and formally incorporated into its Bylaws.

SWGDAM Enhanced STR Detection Guidelines

QUESTION: The document contains a fallacy that low copy DNA is a method not an amount.  Low copy or low template refers to an amount of DNA.  That amount should be stated in this document and it is 100-200 pg, based on numerous scientific and internal validation studies.

SWGDAM Response: SWGDAM concurs that “low copy DNA” does literally refer to an amount of DNA recovered from a limited number of cells that yield a small number of allelic copies for a given genetic locus.  In our Guidelines for STR Enhanced Detection Methods, SWGDAM simply chose to employ the colloquial meaning of the term Low Copy Number Analysis as it is currently used by the forensic DNA testing community to indicate methods used for the purposes of increasing target signal for samples with low DNA template quantities.  These guidelines recognize that any conventional DNA typing method can be used on low levels of template DNA.   The document seeks to designate for special consideration those methods in which a standard method has been modified in such a way as to increase its overall sensitivity to the extent that stochastic phenomena must be taken into consideration.  SWGDAM felt that to strictly base its definition of low copy on a DNA mass (e.g., 100-200 pg) could have unintentionally oversimplified the several mechanisms by which a low copy sample can be obtained (e.g., degradation, inhibition, a minor contributor to a mixture, etc.).  In such samples, the DNA quantity can quantify safely in the non-low copy DNA range (e.g., 1 ng), but if an STR enhanced detection method is employed to overcome any low signal obtained using a conventional method, stochastic results can be detected.

QUESTION: The document [ignores] the issue of replicates.  The scientific literature is very clear.  Replicate analysis must be used when performing enhanced detection methods.

SWGDAM Response: Replicate testing is addressed in Section 4.1 of the SWGDAM Guidelines for STR Enhanced Detection Methods.  It is recommended for Low Template or Low Copy DNA Analysis which SWGDAM has cataloged as a special subset of enhanced detection methods.

SWGDAM Membership

QUESTION: How can I become a member of SWGDAM?

SWGDAM Response (Updated 08/2023): Sections II.C, II.D, and II.E of the SWGDAM Bylaws (approved September 2022) have been revised to update SWGDAM’s business process for appointing members, inviting guests, and engaging subject matter experts (SME).  Generally, SWGDAM receives nominations for participation from current SWGDAM participants or electronically via SWGDAM Contact Us and they are provided to the SWGDAM Vice Chair who chairs the SWGDAM Membership Committee.  The SWGDAM Vice Chair then contacts those individuals to gather their basic professional information via a straightforward application and the applicant’s CV.  The SWGDAM Membership Committee regularly reviews these applications and makes recommendations to the SWGDAM Chair as prescribed in the SWGDAM Bylaws.

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SWGDAM Response: Section II.C of the SWGDAM Bylaws describes the formal business process for appointing SWGDAM members.  Currently, the SWGDAM Membership Committee receives nominations in the form of e-mail requests from the SWGDAM Chair that are either submitted directly to the Chair or through SWGDAM.org or another SWGDAM member/invited guest.  Each request must contain supporting professional information (such as a CV) for the individual requesting consideration for SWGDAM Membership.  Membership appointments are made on an as needed basis and are driven by the needs of SWGDAM as it carries out the responsibilities contained in its Bylaws.

SWGDAM Guidelines

QUESTION: SWGDAM recently published a “recommendation” [Recommendations of the SWGDAM ad Hoc Working Group on Genotyping Results Reported as Likelihood Rations].  Why wasn’t this [made] available for public comment before it was published?
 

SWGDAM Response (12/2018):  Section V.C.5 of the SWGDAM Bylaws states:

5. The committee will submit the final report to the Executive Board.  If the final report is a guidelines or standards document and the Executive Board approves the report for public comment, the Chair will, at a minimum, post the final report on the SWGDAM website for public comment for a minimum of 30 days.  Any comments received during the comment period will be submitted to the committee for consideration.

If a SWGDAM document is something other than a “guidelines or standards document” such as a SWGDAM recommendation, position statement, white paper, letter. etc., the SWGDAM leadership may determine that it is appropriate that the document be subjected to all, none, or only part of the review process prescribed in the SWGDAM Bylaws (Section V.C).  Additionally, in circumstances in which a change(es) made to a SWGDAM guideline document is/are deemed to be non-substantive by the SWGDAM leadership, such changes may or may not be subjected to all of the review elements of its bylaws.

QUESTION: I have noticed that in some commission reports, DNA presentations, and product descriptions statements are made that SWGDAM has reviewed or is aware of the content being discussed or that the content is in accordance with SWGDAM guidelines.  It is clear to me that most often this mention is made either to directly or indirectly suggest that SWGDAM endorses or agrees with the content or conclusions.  [What is the process for seeking SWGDAM endorsement or concurrence?]         
                                                                                 

SWGDAM Response: SWGDAM’s mission as published in its bylaws is to provide guidance to the forensic DNA community on emerging issues and technologies as well as provide recommendations to the FBI Director for revisions to the Quality Assurance Standards.  To accomplish this mission, SWGDAM routinely solicits input from its members, invited guests, and others using a variety of methods to include presentations made at its regular meetings, dialogs made via SWGDAM.org, solicitation of public comments during the development of its guidance documents, and discussions at update sessions at professional meetings.  The sole purpose of these activities is to help better inform SWGDAM’s discussions and work product.  SWGDAM is neither positioned nor sanctioned to evaluate the merits of individual ideas, referee different procedural options, or to endorse products whether that idea, procedure, or product is presented by a SWGDAM participant or other individual.  While SWGDAM has been made aware of situations like the ones cited [not listed here], it does not routinely respond directly to such notifications nor does it investigate incidents or pursue clarifications in the source materials.

QUESTION: I am reading a SWGDAM standard and am in need of some clarification. The details of my question are below and I would appreciate a response.                                                                                          

SWGDAM Response: Neither SWGDAM nor its individual members or invited guests are able to referee individual interpretations or applications of specific elements of any of its guideline documents.  While individual scientists may feel the guidance for any one element unclear or incomplete, SWGDAM has made its best attempt to express the general intent of each element as clearly as possible.  Like all such inquiries, this comment will be discussed internally by SWGDAM to determine if it may be of value to revise a guidelines immediately, develop a general response as an FAQ to share with the forensic DNA community as a whole, or retain it for consideration during its next revision cycle for a document.  As with all such operational inquires, SWGDAM recommends that forensic DNA professionals discuss the content of any applicable SWGDAM document with their peers across the forensic DNA testing community to help inform their individual decision making.

QUESTION: Since the various SWGDAM Guideline documents are more detailed than the FBI QA Standards, why aren't labs held accountable to the specifics within each of the Guideline documents?                                                               
 

SWGDAM Response: The FBI Director’s Quality Assurance Standards for Forensic DNA Testing Laboratories and the Quality Assurance Standards for DNA Databasing Laboratories (referred to hereafter collectively as the QAS) are the minimum quality assurance requirements to ensure that a laboratory will generate quality results and are required by law for forensic laboratories that participate in the National DNA Index System (NDIS). The standards cover all areas such as the education and experience of personnel working in the laboratory, the validation of analyses and processes used by the laboratory, equipment, proficiency tests, reports, audits and health and safety.  SWGDAM’s principal responsibility is the recommendation of revisions, as required, to these minimum quality assurance standards.
 

SWGDAM also periodically issues new and revises existing guideline documents intended to provide additional best-practice recommendations to the forensic DNA community, consistent with the minimum standards, on relevant new techniques or topics of interest to the DNA community such as data interpretation, validation, and training. SWGDAM will often incorporate elements previously included in a new or revised SWGDAM guideline into its proposed revisions to the QAS for the purposes of elevating that previously identified best-practice to a new minimum standard required for participation in NDIS.  If incorporated as a minimum standard for a quality assurance program, this requirement will be subject to the QAS audit process. As a result, while SWGDAM guidelines may contain a greater level of specificity, be broader in scope, and represent SWGDAM’s recommendations for industry best practices that conform to all existing minimum QAS requirements, it is only the QAS that contain the minimum quality assurance standards for participation in NDIS as assured through the formal auditing process.  It should also be noted that the requirements of the QAS are most often adopted by accrediting bodies and incorporated into their individual assessment criteria for forensic DNA testing laboratories and enforced via the accreditation inspection process.

QUESTION: Has SWGDAM published a set of verbal equivalents for describing likelihood ratios?            

SWGDAM Response: While SWGDAM continues to discuss the reporting of likelihood ratios, it has not published guidance for the use of verbal equivalents or scale of conclusions.  In an effort to assist you in this matter, SWGDAM is aware that at least 2 groups have published information on this topic:  the Association of Forensic Science Providers in Science and Justice 49 (2009) 161-164 and the European Network of Forensic Science Institutes (ENFSI) via its ENFSI Guideline for Evaluative Reporting in Forensic Science entitled Strengthening the Evaluation of Forensic Results across Europe (STEOFRAE) .  Please understand that SWGDAM did not participate in the development of either of these sources nor is it in a position to endorse either document.  SWGDAM is simply providing these potential 2 sources here as points for those interested to continue their search for potential guidance on the existence and use of LR verbal equivalents.

SWGDAM Response (Updated 08/2018):  SWGDAM has issued Recommendations of the SWGDAM Ad Hoc Working Group on Genotype Results Reported as Likelihood Ratios which is available on the SWGDAM Publications Page.

QUESTION: I was wondering if [SWGDAM] will be posting public comments on the SWGDAM Validation Guidelines for Probabilistic Genotyping software?  I am interested in seeing what the forensic community had to say about them.

SWGDAM Response: SWGDAM's Bylaws (V.C.5) do not currently specify that SWGDAM make the public comments it receives available for review upon the completion of the public comment period. In formulating its business model regarding soliciting public comments on its proposed changes to the Quality Assurance Standards (QAS) and its guidance documents, SWGDAM preformed a business analysis on the other 19 Scientific Working Groups (SWGs) in existence at the time and adopted a hybrid model based on the different strategies identified across the spectrum of SWGs.  Currently, SWGDAM solicits public comments, acknowledges their receipt, and forwards them to the committee or working group of interest for consideration.   On occasion, SWGDAM will place a specific comment it receives during the public comment period, together with SWGDAM's response, on the FAQ Page of SWGDAM.org if it believes that a comment may be of special interest to the forensic DNA community.

QUESTION: What are guidelines and how should they be used?

SWGDAM Response: Guidelines recommended by SWGDAM are intended to provide additional guidance to the DNA community on current relevant topics.  These guidance documents are simply that and should not be viewed or treated as requirements or minimum standards for forensic DNA laboratories.  SWGDAM will update guidelines as needed to ensure that such guidance is in accord with the available scientific information and best practices at that time. 

QUESTION: Within many of the SWGDAM guidelines the statement is made that these guidelines are not intended to be used retroactively. What is the intent of this “retroactive” statement?

SWGDAM Response:  SWGDAM includes a “retroactive” statement with the intent that the revised guidance be applied prospectively and not retroactively.  With the underlying assumption that work (validation, training, analysis, interpretation) performed prior to the issuance of the revisions was appropriate and scientifically valid, revision of the applicable guidelines is not intended to invalidate or call into question the previous work.