Familial searching: a specialist forensic DNA profiling service utilising the National DNA Database to identify unknown offenders via their relatives--the UK experience.

The National DNA Database (NDNAD) of England and Wales was established on April 10th 1995. The NDNAD is governed by a variety of legislative instruments that mean that DNA samples can be taken if an individual is arrested and detained in a police station. The biological samples and the DNA profiles derived from them can be used for purposes related to the prevention and detection of crime, the investigation of an offence and for the conduct of a prosecution. Following the South East Asian Tsunami of December 2004, the legislation was amended to allow the use of the NDNAD to assist in the identification of a deceased person or of a body part where death has occurred from natural causes or from a natural disaster. The UK NDNAD now contains the DNA profiles of approximately 6 million individuals representing 9.6% of the UK population. As the science of DNA profiling advanced, the National DNA Database provided a potential resource for increased intelligence beyond the direct matching for which it was originally created. The familial searching service offered to the police by several UK forensic science providers exploits the size and geographic coverage of the NDNAD and the fact that close relatives of an offender may share a significant proportion of that offender's DNA profile and will often reside in close geographic proximity to him or her. Between 2002 and 2011 Forensic Science Service Ltd. (FSS) provided familial search services to support 188 police investigations, 70 of which are still active cases. This technique, which may be used in serious crime cases or in 'cold case' reviews when there are few or no investigative leads, has led to the identification of 41 perpetrators or suspects. In this paper we discuss the processes, utility, and governance of the familial search service in which the NDNAD is searched for close genetic relatives of an offender who has left DNA evidence at a crime scene, but whose DNA profile is not represented within the NDNAD. We discuss the scientific basis of the familial search approach, other DNA-based methods for eliminating individuals from the candidate lists generated by these NDNAD searches, the value of filtering these lists by age, ethnic appearance and geography and the governance required by the NDNAD Strategy Board when a police force commissions a familial search. We present the FSS data in relation to the utility of the familial searching service and demonstrate the power of the technique by reference to casework examples. We comment on the uptake of familial searching of DNA databases in the USA, the Netherlands, Australia, and New Zealand. Finally, following the adverse ruling by the European Court of Human Rights against the UK in regard to the S & Marper cases and the consequent introduction of the Protection of Freedoms Act (2012), we discuss the impact that changes to regulations concerning the storage of DNA samples will have on the continuing provision of familial searching of the National DNA Database in England and Wales.

A comparison of the characteristics of profiles produced with the AMPFlSTR SGM Plus multiplex system for both standard and low copy number (LCN) STR DNA analysis.

DNA STR profiles have been generated from 1 ng and low copy number (LCN) templates using 28 and 34 cycles of amplification, respectively. Characteristics which facilitate the interpretation of profiles, such as heterozygous balance, allelic dropout and stutter proportions have been quantified. We demonstrate that a reduction in DNA template coupled with an increase in amplification cycle number produces an increased rate of allelic dropout out which can be correlated to the peak areas of those alleles observed. In addition, the LCN conditions increase the degree of peak area asymmetry observed from heterozygotes and the size range of stutters. Analysis of the data allows us to develop sets of guidelines appropriate for interpreting both single and mixed DNA profiles.

Spectrum of disease among HIV-infected adults hospitalised in a respiratory medicine unit in Abidjan, Côte d'Ivoire.

SETTING: Respiratory medicine wards of the University Teaching Hospital, Abidjan, Côte d'Ivoire. OBJECTIVES: To describe the spectrum of opportunistic infection among human immunodeficiency virus (HIV) infected adults hospitalised in the respiratory medicine unit in Abidjan, and the level of immunosuppression at which these diseases occur. DESIGN: Cross-sectional study. RESULTS: Overall, 75% of patients were HIV-positive: among these patients, the most frequent diagnosis was tuberculosis, in 61%, followed by bacterial pneumonia (15%), Gram-negative septicaemia (particularly non-typhoid Salmonella) (9%) and empyema (5%). Atypical pneumonias appeared to be rare. Most HIV-positive patients had CD4 counts indicative of advanced immunosuppression: 36% had CD4 counts below 100 x 10(6)/l, 19% between 100 and 199 x 10(6)/l, 29% between 200 and 499 x 10(6)/l, and 16% above 500 x 10(6)/l. Overall in-hospital mortality was 27% for HIV-positive patients and 22% for HIV-negative patients (P = 0.5). In a multivariate analysis, the strongest independent risk factors for death were cachexia (odds ratio [OR] 7.4, 95% confidence interval [CI] 2.1-26.3), male sex (OR 4.5, 95% CI 1.2-17.4) and age over 40 (OR 4.1, 95% CI 1.0-17.2). CONCLUSIONS: Tuberculosis and bacterial infections are the major causes of respiratory morbidity in immunosuppressed HIV-infected adults in this population. Efforts to improve the management of HIV-related disease need to focus on prevention and treatment of these infections.

The Côte d'Ivoire national HIV counseling and testing program for tuberculosis patients: implementation and analysis of epidemiologic data.

OBJECTIVES: To describe the implementation of a free, voluntary and confidential HIV counseling and testing program for patients with newly diagnosed tuberculosis at the eight large outpatient tuberculosis centers in Côte d'Ivoire, and to present epidemiologic findings on participating patients. DESIGN: HIV counseling and testing program with ongoing HIV serosurveillance. METHODS: HIV counseling and testing services were established at the two tuberculosis centers in Abidjan in 1989 and were extended to six centers in the Côte d'Ivoire interior in the first half of 1994. Characteristics of counseled patients, acceptance rates of HIV testing, and HIV serologic results were analyzed for all eight centers from 1994 to 1996. Temporal trends in HIV seropositivity rates were examined for the two centers of Abidjan from 1989 to 1996. RESULTS: From July 1994 through December 1996, 17 946 (91.8%) out of 19 594 patients who were counseled at the eight centers in Côte d'Ivoire consented to HIV testing, of whom 7749 (43.2%) were HIV-seropositive. The highest rates of 47.0 and 45.6% were found in the two centers in Abidjan, with rates ranging from 32.9 to 42.4% in the six centers in the interior. HIV-seropositive tuberculosis patients from each of the 50 districts in Côte d'Ivoire were identified. In Abidjan, the HIV seropositivity rate remained relatively stable among men (46.7% in 1989, 48.5% in 1991, 43.6% in 1996), but rose sharply among women from 32.7% in 1989 to 50.1% in 1996. CONCLUSIONS: The high HIV seropositivity rates among tuberculosis patients in all geographic regions of Côte d'Ivoire indicate that the HIV epidemic has now spread throughout the country. However, the successful implementation of an extensive HIV counseling and testing program for more than 37000 tuberculosis patients to date demonstrates the commitment of the Côte d'Ivoire Ministry of Health to integrating HIV/AIDS prevention activities with tuberculosis control efforts. When logistically and economically feasible, the extension of HIV-related social and clinical services to HIV-seropositive tuberculosis patients should be considered by other national tuberculosis control programs in Africa.

Analysis and interpretation of mixed forensic stains using DNA STR profiling.

The use of multiplex PCR and fluorescent dye technology in the automated detection and analysis of short tandem repeat loci provides not only qualitative information about the profile--i.e. which alleles are present--but can also provide quantitative information on the relative intensities of the bands, and is therefore a measure of the amount of amplified DNA. The availability of this quantitative information allows for the interpretation of mixtures in a detailed way which has not been previously possible with many other human identification systems. In this paper we present a simple approach to the resolution and analysis of mixed STR profiles resulting from the testing of mixed biological stains in forensic casework and highlight factors which can affect it. This approach requires a detailed knowledge--gained through a mixture of experiments and validation studies--of the behaviour of each locus within the multiplex systems described. We summarise the available data from previously published experimental work and validation studies to examine the general principles underlying this approach.

Impact of the 1994 expanded World Health Organization AIDS case definition on AIDS surveillance in university hospitals and tuberculosis centers in Côte d'Ivoire.

OBJECTIVE: To assess the impact of the 1994 expanded World Health Organization (WHO) AIDS case definition on AIDS surveillance in Côte d'Ivoire. DESIGN: Prospective AIDS case surveillance. METHODS: From March 1994 through December 1996, passive AIDS case surveillance was conducted at the three university hospitals in Abidjan, and active AIDS case surveillance was conducted at the eight tuberculosis (TB) centers in Côte d'Ivoire. Standardized questionnaires were administered and blood samples for HIV serologic testing were collected from the patients evaluated. The numbers of persons who met the modified 1985 WHO clinical AIDS case definition (Bangui definition) and the 1994 expanded WHO AIDS case definition were determined, and the clinical characteristics of these patients were assessed. RESULTS: Of 8648 university hospital patients, 3658 (42.3%) met the clinical and/or the expanded case definition: 744 (20.3%) HIV-seropositive persons met only the expanded definition, 44 (1.2%) HIV-seropositive persons met only the clinical definition, 2334 (63.8%) HIV-seropositive persons met both definitions, and 536 (14.7%) HIV-seronegative persons met only the clinical definition. Of 18,661 TB center patients, 9664 (51.8%) met the clinical and/or the expanded definition: 5685 (58.8%) HIV-seropositive persons met only the expanded definition, none of the HIV-seropositive persons met only the clinical definition (by definition), 2625 (27.2%) HIV-seropositive persons met both definitions, and 1354 (14.0%) HIV-seronegative persons met only the clinical definition. CONCLUSIONS: Because of the inclusion of multiple severe HIV-related illnesses into the expanded definition, the number of reportable AIDS cases in HIV-seropositive patients increased 31.3% in the university hospitals, and 217% in the TB centers. The inclusion of HIV seropositivity as a criterion for the expanded definition also enhanced the specificity of AIDS case reporting, eliminating 536 cases in the university hospitals and 1354 cases in the TB centers in HIV-seronegative patients who had clinical signs of AIDS. The use of the 1994 expanded definition for surveillance purposes should be encouraged in areas of the developing world where HIV serologic testing is available.

The associations between cervicovaginal HIV shedding, sexually transmitted diseases and immunosuppression in female sex workers in Abidjan, Côte d'Ivoire.

OBJECTIVE: To measure the frequency and associated factors of cervicovaginal HIV shedding and to determine the impact of sexually transmitted disease (STD) treatment on HIV shedding. DESIGN: Cross-sectional study with 1-week follow-up. SETTING: Confidential clinic for female sex workers in Abidjan, Côte d'Ivoire. PARTICIPANTS: A total of 1201 female sex workers. INTERVENTIONS: STD treatment based on clinical signs. MAIN OUTCOME MEASURES: HIV serostatus; cervicovaginal HIV shedding at enrollment and at 1-week follow-up; STD status at enrollment and at 1-week follow-up. RESULTS: Cervicovaginal shedding of HIV-1 in HIV-1-seropositive women was more frequent (96 out of 404, 24%) than shedding of HIV-2 in HIV-2-seropositive women [one out of 21, 5%; odds ratio (OR), 6.2; 95% confidence interval (CI), 1.0-261]. Among 609 HIV-1-seropositive or dually seroreactive women, HIV-1 shedding was significantly more frequent in immunosuppressed women [adjusted OR (AOR), 6.3; 95% CI, 3.4-11.9; and AOR, 2.9; 95% CI, 1.6-5.0 for CD4 < 14% and CD4 14-28%, respectively, versus CD4 > 28%], and in women with Neisseria gonorrhoeae (AOR, 1.9; 95% CI, 1.2-3.0), those with Chlamydia trachomatis (AOR, 2.5; 95% CI, 1.1-5.8), and with a cervical or vaginal ulcer (AOR, 3.9; 95% CI, 2.1-7.4). HIV-1 shedding decreased from 42 to 21% (P < 0.005) in women whose STD were cured. CONCLUSIONS: These data help to explain the difference in transmissibility between HIV-1 and HIV-2 and the increased infectiousness of HIV in the presence of immunosuppression and STD. In addition, they lend biological plausibility to arguments for making STD control an integral part of HIV prevention strategies in Africa.

Profound immunosuppression across the spectrum of opportunistic disease among hospitalized HIV-infected adults in Abidjan, Côte d'Ivoire.

OBJECTIVES: To describe the spectrum of opportunistic disease in HIV-infected patients admitted to hospital in Abidjan, Côte d'Ivoire, and to describe the level of immunosuppression at which these diseases occur. DESIGN: Cross-sectional study. SETTING: In-patient wards of the University Hospital Infectious Diseases Unit. PATIENTS: A total of 250 adult patients recruited by systematic sampling at the point of hospital admission. MAIN MEASURES: HIV status; CD4 count; diagnoses, confirmed by microbiological/radiological investigations whenever possible; and outcome of hospitalization (death or discharge). RESULTS: Overall, 79% patients were HIV-positive. The most frequent diagnoses in HIV-positive patients were septicaemia (20%, with non-typhoid salmonellae, Escherichia coli and Streptococcus pneumoniae the most common organisms), HIV wasting (16%), meningitis (14%), tuberculosis (TB; 13%), isosporiasis (10%), cerebral toxoplasmosis (7%) and bacterial enteritis (7%). Most HIV-positive patients had evidence of severe immunosuppression: 39% had CD4 counts < 50 x 10(6)/l, 17% had 50-99 x 10(6)/l, and 20% had 100-199 x 10(6)/l. In-hospital mortality among HIV-positive patients was 38% compared with 27% among HIV-negative patients [age-adjusted odds ratio (OR), 1.5; 95% confidence interval (CI), 0.7-2.9]. Among HIV-positive patients, the highest case-fatality rates were among patients with meningitis, toxoplasmosis and TB: in a multivariate analysis the strongest independent risk factors for death were an abnormal level of consciousness (OR, 9.3; 95% CI, 3.5-24.6), a haemoglobin concentration below 8 g/dl (OR, 4.2; 95% CI, 1.4-12.8) and age > 40 years (OR, 3.9; 95% CI, 1.5-10.2). CONCLUSIONS: Our data show that, as in industrialized countries, most HIV-infected individuals admitted to and dying in hospital in Abidjan are profoundly immunosuppressed. Potentially preventable infections are the main causes of in-hospital morbidity and mortality among HIV-infected persons in Abidjan, and the evaluation of appropriate primary prophylactic regimes is a priority.

Late postnatal mother-to-child transmission of HIV-1 in Abidjan, Côte d'Ivoire.

BACKGROUND: HIV-1 can be transmitted from an infected mother to her infant through breastfeeding, although the precise risk of transmission by this route is unknown. A long-term follow-up of children born to HIV-infected women in Abidjan, Côte d'Ivoire, has enabled us to estimate this risk. METHODS: Children born to 138 HIV-1-seropositive women, 132 HIV-2-seropositive women, 69 women seroreactive to both HIV-1 and HIV-2, and 274 HIV-seronegative women were enrolled at birth and followed up for as long as 48 months. All children were breastfed (median duration 20 months). Blood samples for either or both HIV PCR and HIV serology were obtained at 1, 2, and 3 months of age, and every 3 months thereafter. Early HIV infection was defined as a positive HIV-1 PCR result obtained in the first 6 months of life. Late postnatal transmission was diagnosed when a child had a negative PCR at 3 or 6 months of age, followed by either or both a positive HIV-1 PCR at 9 months or older, or persistently positive HIV-1 serology at 15 months or older. FINDINGS: 82 children born to HIV-1-seropositive mothers and 57 children born to mothers seropositive for both HIV-1 and HIV-2 had PCR results for samples taken within the first 6 months. By 6 months of age, 23 (28%; 95% CI 19-39) of the 82 children born to HIV-1-seropositive mothers and ten (18%; 95% CI 9-30) of the 57 children born to dually seropositive mothers were HIV-1 infected. Among children whose PCR results were negative at or before age 6 months, and who were followed up beyond 6 months, an additional four (9%) of the 45 children born to HIV-1-seropositive mothers and two (5%) of the 39 children born to dually seropositive mothers became HIV infected. The estimated rates of late postnatal transmission, with account taken of loss to follow-up and the observed pattern of weaning, were 12% (95% CI 3-23) and 6% (0-14), respectively. One of the five children whose mothers seroconverted from HIV-negative to HIV-1, and one of seven children whose mothers seroconverted from HIV-2 to dual reactivity, became HIV-1 positive. No case of late postnatal transmission occurred in children born to HIV-2-positive or persistently HIV-negative mothers. INTERPRETATION: Breastfed children born to mothers seropositive for HIV-1 alone or seropositive for HIV-1 and HIV-2 in Abidjan are at substantial risk of late postnatal transmission. Early cessation of breastfeeding at 6 months of age should be assessed as a possible intervention to reduce postnatal transmission of HIV.

Further validation of a quadruplex STR DNA typing system: a collaborative effort to identify victims of a mass disaster.

The relatively new, PCR-based technique of Short Tandem Repeat (STR) profiling has been used in the identification of the victims of a mass disaster. The analysis relied upon a recently developed multiplex reaction and the use of automated fluorescence technology to simulataneously analyse four tetrameric STR loci. The performance of the 'quadruplex' test was assessed by use of a collaborative study incorporating a blind trial and was demonstrated to be accurate, reliable and robust. Furthermore, the system proved to be highly successful despite the fact that many of the samples from the mass disaster scene were extremely degraded. The high success rate coupled with the discrimination power of the system enabled many severely decomposed human remains to be positively identified.

Identification of bodies from the scene of a mass disaster using DNA amplification of short tandem repeat (STR) loci.

The accompanying paper in this issue describes work conducted during a collaborative effort to identify the victims of a mass disaster that occurred on the 19th of April 1993 near Waco, Texas. The DNA identification programme was also used partly as an exercise to further investigate the robustness and reliability of a recently developed STR quadruplex. The preceding paper provides details of the loci used and also deals with efforts to assess the applicability of STR profiling and its suitability for forensic investigations of this nature. In this paper, we present the results obtained from 61 Waco bodies. Using reference blood samples and family trees 26 positive identifications were made using a 'paternity style' analytical approach. Worked examples, representing a range of casework situations, are used to illustrate the kind of approach taken in interpretation of the data and highlight factors which affected its success. Additionally, we report on the successful application of a PCR-based gender test to 24 of the Waco bodies.

Short tandem repeat typing of bodies from a mass disaster: high success rate and characteristic amplification patterns in highly degraded samples.

We have used a PCR-based DNA-typing method, involving the coamplification of four tetrameric short tandem repeat loci, in the analysis of a large number of severely degraded tissue samples taken from the scene of a mass disaster in which bodies were exposed to extreme thermal, physical and chemical insult. Analysis of the amplified DNA in a number of the samples revealed uniquely sized artifact PCR products resulting from the amplification of degraded genomic DNA as well as characteristic patterns in the amounts of PCR products generated from differently sized loci. This system has proved to be very reliable and robust, and we were successful in typing all of the four loci in 66% of the samples tested and at least one locus in 83% of the cases. A PCR-based sex test also proved to be very effective when applied to the degraded samples.

Prospective comparison of mother-to-child transmission of HIV-1 and HIV-2 in Abidjan, Ivory Coast.

OBJECTIVE: To compare mother-to-child transmission of human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2, respectively) and to assess the impact of maternal HIV-1 and HIV-2 infections on child survival. DESIGN: Prospective cohort study. SETTING: Maternal and child health center in a lower socioeconomic class district of Abidjan, Ivory Coast. PARTICIPANTS: A total of 18,099 women delivering between 1990 and 1992 were tested for HIV-1 and HIV-2 antibodies. A cohort of 613 pregnant women and their infants was followed prospectively (138 women reactive to HIV-1, 132 reactive to HIV-2, 69 reactive to both viruses, and 274 HIV-seronegative). MAIN OUTCOME MEASURES: Rates of perinatal transmission for HIV-1, HIV-2, and both viruses, determined from results of serological and polymerase chain reaction tests on children; survival of infants born to HIV-1-positive, HIV-2-positive, dually reactive, and HIV-seronegative women. RESULTS: Of the 18,099 women tested, 9.4% were reactive to HIV-1 alone, 1.6% to HIV-2 alone, and 1.0% to both viruses. The rate of perinatal transmission of HIV-1 was 24.7% (95% confidence interval [CI], 15.8% to 33.7%), compared with 1.2% (95% CI, 0.0% to 3.5%) for HIV-2 (relative risk, 21.3; 95% CI, 2.9 to 154.3). Overall, 19.0% (95% CI, 9.0% to 29.0%) of infants of dually reactive women became infected; of the 11 children concerned, 10 were infected with HIV-1 and one with HIV-1 and HIV-2. Infants of HIV-seropositive mothers had a reduced survival; mortality rates were 15.1, 13.0, 6.5, and 3.4 deaths per 100 child-years, respectively, for children of HIV-1-positive, dually reactive, HIV-2-positive, and HIV-seronegative women. CONCLUSIONS: The rate of perinatal transmission of HIV-2 (1.2%) was much lower than the rate of perinatal transmission of HIV-1 (24.7%), and this was associated with more favorable survival for infants of HIV-2-infected mothers. Dually reactive women could transmit both viruses, although transmission usually involved HIV-1 only. Public health guidelines should incorporate advice that perinatal transmission of HIV-2 is rare.

The validation of short tandem repeat (STR) loci for use in forensic casework.

A quadruplex reaction has been developed which amplifies the short tandem repeat (STR) loci HUM-VWA31/A, HUMTHO1, HUMF13A1 and HUMFES/FPS. Detection of the PCR products employs denaturing polyacrylamide gels coupled with fluorescent-based technology. This system has been evaluated for use in routine forensic casework and has been shown to be both robust and reproducible. The quadruplex reaction is as sensitive as the commercially available HLA DQ alpha Amplitype typing system and can be used on both degraded and aged material. The problems of environmental contamination have been shown to be limited provided strict procedural practices are followed-i.e. physical separation of sample extraction and amplified products; the use of dedicated equipment such as pipettes; the separation of amplification preparation area. The ability of the system to detect mixtures and the successful analysis of case stains has shown that this system is well suited as a tool for forensic investigation.

Racial differences in survival of women with breast cancer.

The hypothesis that white women with breast cancer survive longer than black women with this disease was evaluated in a retrospective analysis of a population-based prospective follow-up study. All female residents of metropolitan Atlanta with a first diagnosis of primary breast cancer between 1 January 1978 and 31 December 1982 were eligible for inclusion. The study population of 2322 white and 536 black women was followed through the end of calendar year 1983 to determine vital status. Univariate, multivariate and excess death rate analyses were performed to evaluate race as a prognostic factor. Overall, the cumulative percentage of survivors at 3 years was 83% among whites, compared with 71% among blacks. The racial difference in survival was greatest among women with advanced disease, and a higher proportion of black women with advanced disease did not receive surgery. Even when the type of surgery and stage of disease were controlled, race was a significant prognostic factor.

Cancer incidence rates among blacks in urban and rural Georgia, 1978-82.

The records of the Atlanta Cancer Surveillance Center were reviewed for all incident cases of cancer diagnosed among Black residents of the catchment areas during calendar years 1978 through 1982. The resultant age-adjusted overall cancer incidence rates for urban Blacks were greater than those for rural Blacks. The largest urban excess was found for cancers of the buccal cavity and pharynx. Urban residence also was associated with lung and prostate cancers among males, and pancreatic cancers among females.