Forensic Genetics Studies On Two West African Populations:DNA Databases And Genetic Structures In Burkina Faso And Sierra Leone

Background:In the past 20 years,the development and application of forensic physical evidence have completely changed forensic science.One of the keys is the use of short tandem repeat（STR）sites in human identification,which is also the preferred forensic heritage identification technology at present.In fact,STRs,also known as microsatellites,is a short tandem repeat DNA sequence,which forms a sequence with a length of about 100 nucleotides through a repeat unit of 2-6bp.Thousands of STRs have the potential for forensic analysis.STR loci are distributed in the whole genome,including 22 autosomal and the sex chromosomes（X and Y）.Most STRs used in forensic physical evidence are tetranucleotide repeats.STRs meet almost all the requirements of forensic scientists for forensic genetic markers:they are stable and can analyse all kinds of biological samples;The results produced by different laboratories are easy to compare;They are highly polymorphic,and the commonly used loci contain many alleles;They are very sensitive and require only a few cells to be successfully analysed;It is relatively cheap and easy to generate STR map,and there are a large number of STRs in the whole genome.STR is usually amplified by commercial multiplex PCR kit and alleles are detected by capillary electrophoresis（CE）.The 20 genetic markers of the DNA core index system（CODIS）recommended by the FBI laboratory and 17 core loci used in the UK and Europe have become the core loci of the forensic STR kit.STR detection can also be used to investigate missing persons and identify victims of large-scale disasters.However,although Africa is the second largest continent in terms of area and population,and includes many countries（54）and different races,there are few forensic population genetic data studies on these groups.Therefore,it is very necessary to obtain the genetic data of these populations.Objectives:This study’s primary purpose was to establish a comprehensive reference forensic allelic frequencies database for forensic and population genetic analyses in two West African countries,Burkina Faso and Sierra Leone.Methods and Results:This thesis is divided into five chapters:The first chapter,which stands as the background of this thesis,focused on the steps that lead DNA typing systems to the stage of gold standard practice in forensic genetics according to the literature review.The second chapter is focused on the BF population and was entitled:“Paternal lineage and first forensic parameters investigation of 29 Y-STR loci in Burkina Faso population ethnic groups”.Indeed,BF named Upper Volta by French settler until August 4,1984 is a Sahelian country located in the heart of West Africa;bordered by Mali in north and northwest,by Niger in the northeast,by Benin in the southeast and by Cote d’Ivoire,Ghana,and Togo in the south.BF has a population over 20.9 millions according to Institut National de la Statistique et de la Démographie（ISND）of BF.Ouagadougou is the capital of BF and its largest city.The languages spoken are French（official）and several other native languages.Most of the native languages spoken today in BF（63 out of 68）belong to one of two prominent families of the Niger-Congo phylum:either Mande or Gur（Voltaic）.About 90%of the Burkinabe population speak Moore,Fulfulde,and Dioula.To clarify the significance of a match between genetic profiles in forensic cases,forensic parameters for the concerned population in question must be known.The alternative of using Y-STR is particularly important when standard autosomal DNA profiling is not informative.Previous studies in Africa evidenced complex genetic features.Therefore,the results gained from a few ethnic groups cannot be extrapolated.For accurate application in forensic investigation and for the purpose to obtain a reliable picture of West African genetic diversity,additional human group study still needs to be done.However,none of these two countries in West Africa has a DNA database.To our knowledge,no survey of forensic parameters of 29 Y-STRs loci datasets has been done in BF.In order to pave the way,we successfully typed 447 DNA samples for a cocktail of 29 Y-STRs loci and computed the forensic parameters.The analysis of molecular variance（AMOVA）test allowed a comparison within BF ethnic groups and between the BF population and 13 other African countries.This work aimed to determine the forensic parameters of 29 Y-chromosome STRs polymorphic loci in the BF population and infer the paternal lineage by the haplogroup distribution of males from BF based on the Power Plex^?Y23 System loci.Moreover,in this study,we provided tools to create a forensic database on Y-STRs and genetic sources for studying human population history.As a result,none of these 447individuals in total shared a common haplotype.The overall Y-STR haplotypes resulting are available online on Y-STR Haplotype Reference Database（YHRD）with the accession number YA004690 and YA004691.The main haplotype diversity（HD）was:0.9999999965,which is much higher than that obtained with 12 Y-STRs from the previous study.Haplotype Match Probability（HMP）for the whole data was:0.002237.Pairwise population distance comparisons with 49 subpopulations living in Africa showed that F_ST value was less than 0.25 for overall neighbouring countries to Burkina Faso,indicating no substantial genetic substructure.Haplogroup distribution assignment was inferred by means of the software named Nev Gen based on the Power Plex^?Y23 System loci haplotypes,and E1b1a was the most frequent（98%）.The data displayed in this study will help to establish the Burkina Faso haplotypes frequencies DNA database for population genetic and forensic studies.This work has been published,and it’s available online through this link:10.1007/s00414-021-02544-9.The third chapter,entitled:“Population genetics structure and forensic parameters revealed by 21 autosomal STR loci and 19 X-STR loci in the Burkina Faso ethnolinguistic population”,is focused in its part“A”on the autosomal STRs markers investigation in the BF population.Based on the investigation results in chapter two,we stated that a DNA profile might be more common in one population than another.It’s well known that the genetic characteristics indeed depend on the ethnic origin of the person.Despite its high diversity,the BF population remains poorly investigated,and updated forensic parameters with a large number of autosomal chromosome short tandem repeats（STRs）were still missing.To pave this way,396 unrelated individuals（272 males and 124 females）in BF,were genotyped using the Microreader^TM21 ID System kit.As a result,no locus deviated from HWE after Bonferroni correction（setting p-value（?）0.05/21≈0.0023）.Overall,there were 281 unique alleles with allele frequencies ranging from 0.0013 to 0.4280.The combined power of exclusion for duos（CPE duos）and exclusion for trios（CPE trios）for the 20 tested loci were0.999999837 and 0.999930699,respectively.The probability that two individuals would share the same DNA profiles among the BF population is 5.58955×10^-26.The forensic parameters and genetic structure based on21 autosomal STR loci showed that these alleles frequencies database could be useful for forensic casework and also for population genetic study.A comparison with other African subpopulations published data showed that the BF-Mande ethnolinguistic group has a closer genetic relationship with Nigerian-Haoussa.At the same time,the BF-GUR population were slightly close to Nigeria-Igbo,Nigeria-Yoruba,Sierra Leone,and South Africa-SEB.In part“B”of chapter three,we have investigated forensic parameters and genetic structure based on 19 X-STR for the first time in the Burkina Faso population.A total of 292（169 Males and 123 Females）individuals have been involved in this study.As a result,among the 19 X-STR loci,no significant deviations from the Hardy-Weinberg equilibrium were observed in female samples after Bonferroni correction p<0.05/19=0.0026 except for the locus GATA165B12 and DXS7423.The combined Power of Exclusion（CPE）,the combined power of discrimination in females（CPD_F）and males（CPD_M）were 0.999999760892967,0.999999999992047,and 1,respectively.Therefore,the mean paternity exclusion chances（MEC）based on the formula of MEC_Krüger,MEC_Kishida,and MEC_Desmarais,as well as MEC_{Desmarais Duo} were 0.999999930181708,0.999999999990194,0.999999999990369,and 0.999999983891293,respectively.A comparison between the BF population and reference population based on ten loci shows that BF-Mande speakers are close to Sierra Leone individuals living in Freetown.In contrast,the BF-Atlantic languages speakers tend to be genetically unrelated to BF-Mande and Gur speakers.The fourth chapter of this thesis is mainly dedicated to the Sierra Leone population.As we mentioned earlier,a research collaboration between Sierra Leone scientific and our laboratory allowed us to investigate the population’s genetic structure in Freetown,Sierra Leone.The results of this collaboration have been published in two different research papers.The first part,“A”,of this chapter entitled:“Forensic Genetic characterisation of 19 X-STRs in Sierra Leone population from Freetown”,described the results generated using highly polymorphic forensic markers of 19 X-STRs from a commercial kit.This specific part result has been submitted to peer review,and the resulting research paper can be found online with the link DOI:10.1007/s00414-019-02243-6.The second part,“B”,of this chapter entitled:“Forensic parameters and genetic structure analysis of 30 autosomal In Dels of the population in Freetown,Sierra Leone”,was focused on the genetic structure of the same set of individuals from the population in Freetown revealed by using 30 highly polymorphic autosomal In Dels forensic markers.The results of this work also have been published in the International Journal of Legal Medicine and can be found with the link DOI:10.1007/s00414-020-02417-7.As mentioned previously,Sierra Leone is a West African country bordered by the Republic of Guinea in the North and northeast,Liberia in the East and southeast,and the Atlantic Ocean in the west and south.The country name comes from Pedro de Sintra,a Portuguese explorer.During the 15th century,Pedro de Sintra was the first to sight and map the Freetown harbour.Freetown is Sierra Leone’s capital,and it commands one of the largest natural harbours in the world.In the transatlantic slave trade,the country was one of the departure points for thousands of enslaved people from West African captives.According to the story,the capital Freetown was founded in 1787 as the home for repatriated formerly enslaved people.To date,Sierra Leone is a multicultural country with 18 ethnic groups with similar cultural features.Indeed farming methods,patrilineal descent,and so on are in common in the society ethnic groups.The significant historical position and the multicultural society are the reasons that lead us to investigate the Sierra Leone population genetic structure.In the first section of chapter 4,we investigated 19 X-STR markers.The multicultural society encountered in the country leads us to explore the genetic characterisation of 550 individuals.We investigated a group of individuals with 265 males and 285 females living in the capital city of Freetown.The commercial kit Microreader^TM19X ID System kit has been used for genotyping the 550 DNA samples.The results didn’t exhibit a significant deviation from the Hardy-Weinberg equilibrium.A number of250 different alleles were identified with corresponding allele frequencies ranging from 0.0012 to 0.6762.The highest PIC was 0.9481,while the lowest PIC of the loci was 0.4615.The CPDM was 0.999999999998997while the CPDF and the CPE were 0.999999999999999999995774 and0.9999997856,respectively.The high combined MECDesmarais Duo,MECDesmarais,MECKishida,MECKruger,were achieved as0.99999998412,0.999999999990836,0.999999999990802,and0.99999992508,respectively.Genetic structure comparisons pointed out genetic homogeneity existing in similar ethnic origin or geographic origin populations.This study is the first genetic investigation using the Microreader^TM19X ID System kit in Sierra Leone’s population from Freetown.In the second section of chapter 4,we then focused on the autosomal insertion/deletion（In Dels）markers.Africa is generally considered the cradle of modern humans.The high genetic diversity encountered in its overall population is the source of the growing attraction from many academic studies.However,despite these high diversities,many countries’population genetics haven’t been described yet.Most of the West African countries are still in this situation resulting in an incomplete description of the region on autosomal In Dels markers.Herein,to pave this way,we screened 30 In Dels loci together from 566 samples from Freetown,Sierra Leone.We then analyses the performance of the combination of 30 In Dels genetic markers and evaluated their forensic properties.Besides,we pointed out the genetic landscape of populations living in the capital（Freetown）of the Republic of Sierra Leone.As a result,considering the linkage disequilibrium（LD）after Bonferroni correction,no significant LD between the 30 loci was observed.The combined power of exclusion for trios（CPE trios）,the random match probability（RMP）,the combined power of exclusion for duos（CPE duos）were 0.9731,6.823×10-11,and0.9168,respectively.These panels can also be used to perform better efficiency in paternity testing in West African populations because the 30In Dels were under linkage equilibrium.A comparison of the Sierra Leone population with other populations in Africa demonstrated that the West African populations have the closest genetic relationship except for Yoruba in Ibadan from Nigeria and also the immigrant populations in America.The comparison between the coastal people of Africa and the African continent’s inland population showed that the coastal groups tend to have closer genetic relationships.This can be interpreted as the genetic imprint of the history of Freetown and also as the manifestation of recent immigration.The Fifth chapter of this thesis was focused on the BF population’s opinions about the DNA fingerprint in the criminal justice system.The reason for the interest in public opinion is that since January 2016,following the Cappuccino and Hotel Splendid attacks claimed by terrorist organisations,the security situation in BF has undergone a remarkable turnaround.Following that,the country has been subjected to a series of terrorist attacks in its north and east areas,many of which have resulted in devastating repercussions.After that,the security system has constantly evolved in an attempt to deal with this new threat,which the BF population estimated at more than 20 million,only knew about through media,action films.This adaptation of the security system requires the implementation of new technology,providing scientific solutions that are currently available.DNA identification has been considered and still considered as the gold standard of forensic science in the human identification field.Thereafter,DNA profiling and the use of DNA databases have been the most commonly used investigative techniques in the world.Today,the major trend is the matching or comparison of DNA profiles from crime scenes with those stored in criminal or offender’s DNA databases.This is one of the most significant crime-fighting inventions in modern human history,supplying critical information and saving cops time and resources.However,while DNA databases are widely welcomed,it also raises concerns about privacy,data security,and fairness.What is the status of this DNA technology in BF?DNA testing for forensic purposes is not yet a very common practice in judicial proceedings in BF,despite the need and growing demand.According to an INTERPOL report published in 2020,only eleven（11）countries in Africa use DNA profiling in police investigations.Among these,just seven（07）reported having a DNA database.In West Africa,only the Republic of Ghana and BF acknowledged are using DNA profiling in police investigations.However,none of these two West African countries has a national DNA database to support criminal investigations.In the particular case of Burkina Faso,there is a lot of work to do at the level of the Police Technique Scientifique（PTS）.PTS is the national Police department in charge of forensic investigation in Burkina Faso.Although this department has the qualified human resources to carry out the task,the state institutions in charge of security,i.e.the national Police and the Gendarmerie,do not have the technical platforms for such a purpose yet.Speaking of state institutions,it is nowadays recognized that the advent of technology surrounding human DNA-based identification is an excellent asset for the work of the actors of the judicial chain.What does the law in Burkina Faso state about using DNA data in criminal cases by actors of the criminal justice system?From a legislative point of view,it must be said that BF’s laws are sufficiently permissive regarding the use of scientific processes as a means of proof.Regarding personal status（recognition of paternity,filiation and so on）,we can cite articles 446,454,456,720 of the current personal and family code in place.In this document,Article 446,for example,stipulates that:“When,by application of legal provisions,a child is attached to several fathers,the courts shall settle the dispute by determining by all means of proof the most likely paternity.In the absence of sufficient evidence,they shall have regard to the possession of status”.These provisions provide for the possibility of using any means to prove the existence or not of a fact.The use by the law of the words"all means"allows recourse to scientific evidence.In general,it is these texts or articles that lawyers,the prosecutors,target when ordering a DNA test,for example,in matters of a paternity dispute.Besides,in criminal cases,provisions 252-3,261-104 and following of the Code of Criminal Procedure also allow recourse to scientific procedures by ordering an expert report as a method of proof.As such,article 253-2 of the Burkina Faso code of criminal procedure stipulates as follows that:“Any investigating or trial court in the event that a technical question arises may,either at the request of the public prosecutor,either systematically or at the request of the parties,order an expert report.The experts carry out their mission under the control of the investigating judge or the magistrate to be designated by the court which ordered the expertise.When the investigating judge considers that he should not grant a request for expertise,he must issue a reasoned order,which may be appealed in the forms and time limits provided for in article261-133 of this law”.Apart from these openings made by Burkina Faso legislation to exploit genetic fingerprints,there are not yet specific laws in this area dedicated to the use of DNA fingerprints.According to some reports from the Burkinabe Ministry of Justice,many judgments have not taken place or did not get a satisfactory outcome due to the lack of local expertise in DNA fingerprinting.In a developing country where everything seems to be a priority,combined with the new security challenges that threaten the country’s stability,it seemed essential to us to probe the public’s opinion on the use of genetic fingerprints in BF.For this purpose,we,therefore,designed a survey through a questionnaire dedicated to the Burkinabe public living in the country.Our survey was directed mainly towards three groups:the“Experts and Professionals”of forensic medicine and the criminal justice system,the“Insiders”or the persons well informed of the forensic DNA fingerprint topic,and the“Laymen”considered unfamiliar in the forensic field and not well informed about the forensic DNA fingerprint topic.The main objective of our study was to find out the public’s opinion on the following question:“What do you think about the creation of a national DNA database in Burkina Faso to support forensic investigations?”Another specific objective of this survey was to know who should keep and manage a possible national genetic database in BF to support criminal investigations led by the National Police and Gendarmerie.The results of the survey revealed that 91.7%（431/470）of participants believe that this technology is essential and necessary for Burkina Faso’s criminal justice system.Among the respondents,93.6%of them also felt that the national security services（Police and Gendarmerie）should be provided with forensic science laboratories,especially genetic laboratories capable of performing genetic fingerprints.However,72.3%were against the implication of the private sector in the processing of forensic DNA tests,a limited majority（45.3%）among the respondents suggested that the custody and the management of a national DNA database should be delegated to an independent state agency other than the national security services.On the contrary,36%were categorically against such a position and would instead entrust the national DNA database to the national security services.The results of this survey could guide decision-makers regarding a possible project aiming to set up a national DNA database to support criminal investigations in BF.Conclusion:This thesis describes in detail the genetic research on the populations of Burkina Faso and Sierra Leone.Our research on the population of West Africa has obtained the genetic data of Y chromosome,X chromosome and autosomal of Burkina Faso population and the genetic data of X chromosome and autosomal In Dels of Sierra Leone population,which provides important data support for the forensic DNA identification of the two countries.At the same time,the questionnaire survey of local people in Burkina Faso has obtained the support conclusion of local people for the application of DNA technology to criminal investigation.