We have blogged before on some issues in DNA and in terms of CODIS and the var­i­ous DNA databases:

• DNA Con­t­a­m­i­na­tion that is amazing!
• Another exam­ple of flat out bad foren­sic sci­ence: Bad DNA results
• Bayesian Based Metrol­ogy and DNA
• What con­sti­tutes a “match” in foren­sic science?
• Phys­i­cal evi­dence is often the most impor­tant evidence

Now there is a change com­ing to the way that CODIS is being used as pushed from from the FBI. Not every­one is happy about it. Here is the arti­cle “FBI’s DNA data­base upgrade plans come under fire” By Paul Rin­con Sci­ence edi­tor, BBC News website:

A major upgrade of the Fed­eral Bureau of Investigation’s (FBI) DNA data­base sys­tem has come under fire from mem­bers of the foren­sic sci­ence community.

The Codis sys­tem is used to gen­er­ate the genetic pro­files stored in the US national DNA database.

The FBI wants to expand the num­ber of genetic mark­ers used by Codis to clas­sify indi­vid­ual DNA profiles.

But a for­mer sci­ence chief at the bureau says the plan is not being dri­ven by sci­en­tists’ needs.

Dr Bruce Budowle, along with col­leagues Arthur Eisen­berg and Jianye Ge, out­lined the objec­tions at the Promega 22nd Inter­na­tional Sym­po­sium on Human Iden­ti­fi­ca­tion (ISHI) in Mary­land, US.

Another sci­en­tist told BBC News the changes were vitally impor­tant because they would set down how DNA pro­files were recorded in the United States for per­haps “the next 20 years”.

While work­ing at the FBI in the 1990s, Dr Budowle helped choose the genetic mark­ers cur­rently used by Codis.

Con­sul­ta­tion gap

He says the review is a good idea, but that choos­ing the right mark­ers for foren­sic case­work is crucial.

He told BBC News the FBI did not suf­fi­ciently con­sult with the foren­sic sci­ence com­mu­nity before mak­ing its recommendations.

“The first time around we took a community-wide approach — 21 lab­o­ra­to­ries rolling up their sleeves and gen­er­at­ing data we could analyse and [use to] make deci­sions,” explained Dr Budowle, from the Uni­ver­sity of North Texas Health Sci­ence Cen­ter in Fort Worth.

“This time around, they formed a work­ing group of around five [sci­en­tists] and an FBI per­son to decide what the core set should be.

“Should the needs of Codis — our national data­base sys­tem — drive the case­work processes, or should the needs of case­work drive the Codis processes?

“I would hope the lat­ter is obvi­ously what should be done.”

High pro­file

The US national data­base — the largest in the world — cur­rently con­tains about 10m offender pro­files and has assisted in more than 141,000 investigations.

Codis (which stands for Com­bined DNA Index Sys­tem ) uses a set of 13 genetic mark­ers — known as the “core loci” — to gen­er­ate indi­vid­ual DNA profiles.

In May 2010, the FBI estab­lished a six-strong work­ing group to review the core loci used for data­base searches. It has now rec­om­mended the cur­rent set of 13 mark­ers be increased to 24.

The impor­tance of these mark­ers was demon­strated in the case of a British man arrested in 1999. His DNA pro­file matched that col­lected in a bur­glary when com­pared at six genetic loci.

The sus­pect spent sev­eral months in jail before his lawyer demanded a 10-marker re-test. The sus­pect dif­fered from the bur­glary sus­pect at one of the four addi­tional mark­ers and was set free.

While the prob­a­bil­i­ties of such chance matches between unre­lated indi­vid­u­als are rel­a­tively small, they increase as DNA data­bases grow in size.

In addi­tion, some genetic mark­ers are bet­ter for cer­tain tasks than oth­ers, said Dr Budowle, who pointed to what he said were incon­sis­ten­cies in the selec­tion process for the core loci.

Dr Budowle said some of the mark­ers used in the new and old Codis schemes com­prised such large frag­ments of DNA that they can be dif­fi­cult for foren­sic sci­en­tists to detect in crime scene DNA — which can be prone to degra­da­tion, or may only be present in small amounts.

Even if large frag­ment mark­ers are infor­ma­tive, Dr Budowle said, “if you have degraded sam­ples and you don’t get it, it’s useless”.

He added: “The ana­lysts [in my lab] come to me all the time with dif­fi­cult cases. They say of the large-fragment ones: ‘Get rid of them because they don’t give results’.”

He also said the new scheme passed over infor­ma­tive mark­ers on the Y (male) chro­mo­some which would be use­ful for famil­ial search­ing — a tech­nique used when sci­en­tists can­not find an exact match for a sam­ple in a DNA database.

Famil­ial search­ing relies instead on find­ing close, but not per­fect, matches that might rep­re­sent close rel­a­tives of a suspect.

Loci dif­fi­culty

A spokesper­son for the FBI Lab­o­ra­tory declined to com­ment directly on Dr Budowle’s presentation.

How­ever, Dr Dou­glas R Hares, from the FBI Lab­o­ra­tory in Quan­tico, Vir­ginia, who chairs the Codis expan­sion work­ing group, recently out­lined the bureau’s rec­om­men­da­tions in the jour­nal Foren­sic Sci­ence Inter­na­tional: Genet­ics.

The changes are intended to increase the power to dis­crim­i­nate between indi­vid­ual pro­files and to reduce the like­li­hood of chance matches.

The bureau also wants to increase com­pat­i­bil­ity with inter­na­tional data­bases to enable cross-border infor­ma­tion shar­ing — of increas­ing impor­tance in counter-terrorism.

Dr Hares said the work­ing group had set out objec­tive cri­te­ria for the accep­tance of any new mark­ers, and had con­sulted with the mak­ers of DNA analy­sis kits.

How­ever, Dr Budowle urged the FBI to carry out more research on the per­for­mance of dif­fer­ent mark­ers in past foren­sic inves­ti­ga­tions before set­tling on a new set.

He explained: “If we do the home­work and the data sup­ports that these were the best [mark­ers], that’s great. If it doesn’t sup­port it and we come up with a bet­ter set of mark­ers, that’s equally great.

“Reach out, get a lot of view­points, talk to peo­ple who have a lot of expe­ri­ence. Don’t limit yourself.”

Dr Greg Hampikian, a foren­sic DNA spe­cial­ist from Boise State Uni­ver­sity, told BBC News: “Bruce has raised spe­cific, sub­stan­tive, sci­en­tific issues about the choice of the new loci.

“His point is not that these are bad, but there are bet­ter ones avail­able — specif­i­cally, ones with more power to tell the dif­fer­ence between indi­vid­u­als, and more like­li­hood of detec­tion in degraded sam­ples (since they would detect smaller pieces or DNA).”

Dr Hampikian also backed the inclu­sion of infor­ma­tive Y chro­mo­some mark­ers, par­tic­u­larly in cases involv­ing famil­ial rela­tion­ships and sex­ual assaults. Y chro­mo­some mark­ers have to be analysed sep­a­rately at present, and he said this could result in crit­i­cal lost time in investigations.

“Bruce has become a coura­geous voice for sci­en­tific rigour in foren­sic genet­ics. We have seen some foren­sic prac­tices adopted too quickly, and those result in tragic wastes of pre­cious inves­ti­ga­tion time, wrong­ful pros­e­cu­tions, and more vic­tims,” he said.

A sim­i­lar chal­lenge to that faced by the FBI looms for cus­to­di­ans of the UK’s National DNA data­base (NDAD), which holds about 4m profiles.

The NDAD cur­rently uses 10 core loci to gen­er­ate pro­files; but Pro­fes­sor Sir Alec Jef­freys, who helped pio­neer DNA pro­fil­ing, has rec­om­mended the num­ber be increased to 15 or 16.

Some researchers are con­cerned about the absence of a time­line for upgrad­ing the NDAD, and that, with­out it, the UK risks falling well behind the rest of Europe.