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DNA Used to Identify Man

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楼主
发表于 11-24-2018 13:45:40 | 只看该作者 回帖奖励 |倒序浏览 |阅读模式
Press release: DNA Used to Identify Man Responsible for 1969 Murder of Jane Britton. Middlesex [County] District Attorney, Nov 20, 2018.
https://www.middlesexda.com/site ... _-_jane_britton.pdf

Quote:

"Middlesex District Attorney Marian Ryan announced today that Michael Sumpter, a career criminal with ties to Cambridge has been identified as the person responsible for the 1969 murder of Jane Britton.

"On January 7, 1969 at 12:40 pm, the body of Jane Britton, 23, of Needham[, Massachusetts], a graduate student in Anthropology at Harvard University, was found in her fourth floor apartment, located at 6 University Road, in Cambridge by her boyfriend who came to check on her after she had failed to appear to take an examination that morning. [Naturally police scrutinized the boyfriend among others, but for 5 decades no charge could be filed.]

"In 2017 the Middlesex District Attorney's Office received several requests for the Jane Britton file to be released to the public [which spurred that office into action]. * * * With fresh eyes on the file investigators also sought to determine whether there were any further investigative actions that could be taken, including consulting with the Massachusetts State Police Crime Lab about whether any new advances in forensic DNA technology might be of assistance in yielding a more comprehensive evidence profile.  The decision was ultimately made to perform additional DNA testing with the most up to date testing on the remaining evidence samples. For the first time, the Massachusetts State Police Crime lab was able to obtain a Y-STR, or male-specific profile, from the remaining DNA samples on file from the original swabs [the press release did not say from where, but presumably from vagina] in October of 2017.  In July of 2018 the Massachusetts State Police Crime Lab notified the investigators that there was a match between the 2017 Y-STR profile from the evidence sample and Michael Sumpter's CODIS sample on file with the Massachusetts State Police Crime Lab. Although Sumpter was already deceased, investigators were able to locate [through Ancestry.com DNA database, as disclosed at press conference held by the DA] and obtain a DNA sample from Michael's biological brother who has the same male Y-STR profile. Testing on this sample excluded 99.92% of the male population as a contributor of the DNA and confirmed that Michael Sumpter's profile matched both the original soft hit and the Y-STR profile. Sumpter's brother was excluded as a possible contributor.

"On the day she died, Jane went * * * ice skating with her boyfriend on the Cambridge Common. They also visited Charley's, a pub across from Jane's apartment, before returning to Jane's apartment around 10:30 pm. After her boyfriend left the apartment at around 11:30 pm. Jane then went next door to her neighbors' apartment for a glass of sherry before returning home around 12:30 a.m. The next morning [actually 12: 40 pm, shortly after noontime] she was found dead in her bed.  The Medical Examiner conducted an autopsy on Jane and was able to collect forensic evidence. He ruled that she had been struck by a blunt object multiple times resulting in fractures of the skull, and contusions and lacerations of the brain which were the cause of death. A murder weapon was never positively identified.  Subsequent toxicology testing revealed that her blood alcohol was negative but
her stomach alcohol was 0.08% suggesting that the alcohol she ingested did not have time to metabolize and make it to the bloodstream before death. This indicated that Jane was killed shortly after returning to her apartment [presumably the boyfriend reported to police Jane did not drink at the pub].  On January 7, 1969 a resident of Jane's apartment building reported hearing someone on the fire escape that connected to Jane's apartment earlier on the evening of her murder and a second witness account detailed that a man who appeared to be approximately 6' feet tall and 170 Ibs. was seen running in the street near Jane's apartment at 1:30 am., Mr Sumpter was 5'11" and weighed 185 Ibs. when he was arrested in 1972. It is believed that Mr Sumpter entered Jane's apartment through a window [via fire escape]

"Sumpter was also arrested and convicted of a physical assault on a woman whom he had met at the Harvard Square MBTA station, blocks from Ms Britton's apartment, three years after Jane Britton's murder [in 1972; so this is a different rape that the 1975 one].  This is the third homicide linked to Michael Sumpter since the time of his death. In 2010, the Suffolk District Attorney's Office was informed that Mr Sumpter's DNA was a match to DNA taken from the 1972 murder and rape of 23-year-old Ellen Rutchick in her Beacon Street apartment and in 2012, a second CODIS hit matched Mr. Sumpter to the evidence taken from the 1973 rape and murder of 24-year-old Mary Lee McClain in her Mount Vernon Street apartment. None of the victims are believed to have known, or had any relationship with, Mr Sumpter.   Sumpter had been convicted of committing the stranger rape of a woman in her Boston apartment in 1975. Mr Sumpter died of cancer at the age of 54 in 2001, 13 months after he was paroled from his 15 to 20 year sentence for this 1975 Boston rape. In 2002, after his death, Sumpter was identified by another CODIS hit in connection with a 1985 stranger rape of a woman in Boston committed after Sumpter escaped from work release.  [altogether:] Since his death, DNA testing and the CODIS database identified Michael Sumpter in connection with five sexual assaults, three of which involved the murder of the victim.

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沙发
 楼主| 发表于 11-24-2018 13:46:33 | 只看该作者
本帖最后由 choi 于 11-24-2018 13:49 编辑

Note:
(a)
(i) Attached to the press release, documents 5 to 7 (inclusive) are Jan Britton's photos, and 12, Michael Sumpter's mug shots.
(ii) Combined DNA Index System (CODIS). FBI, undated.
https://www.fbi.gov/services/laboratory/biometric-analysis/codis

(b) The rest of notations are to explain Y-STR. In (b), I will first present a bird's-eye view of "tandem repeat," before focusing on satellite DNA. The (c) will examine two other categories of tandem repeats: micro- and minisatellites. Microsatellite is also known as short tandem repeat (STR), among other names.
(i) Only a few percents of human DNA encodes proteins. Most of the rest has no known function. That does not mean it is junk; we simply do not know its function.
(ii)
(A) "Satellite DNA, together with minisatellite and microsatellite DNA, constitute the tandem repeats."  en.wikipedia.org for "Satellite DNA."
(B) The satellite DNA is the main component of centromeres, to which (centromeres) spindle fibers during mitosis 有丝分裂 or meiosis 减数分裂 attach chromosomes.
(C) The major type of satellite DNA is alpha. See
Sujiwattanarat P et al, Higher-Order Repeat Structure in Alpha Satellite DNA Occurs in New World Monkeys and Is Not Confined to Hominoids. Scientific Reports, 5: 10315 (2015)
https://www.nature.com/articles/srep10315
("Alpha satellite DNA (AS) is the most abundant tandem repeat DNA of primate centromeres, although this may not be true of suborder Strepsirrhini, one member of which (the aye-aye, Daubentonia madagascariensis) is known to carry other unrelated tandem repeat DNA as main components of its centromeres. * * * The length of the repeat units of AS is approximately 170 bp in parvorder Catarrhini, which includes hominoids (superfamily Hominoidea; humans, great apes, and small apes) and Old World monkeys (family Cercopithecidae; macaques, baboons, and related monkeys found in Africa and Asia). * * * The AS of humans, which has been extensively studied for its structural features, is known to contain sequences organized into higher-order repeat (HOR) structures, which are tandem arrays of larger repeat units that consist of multiple basic repeat units. The larger repeat units that have so far been identified include those comprising 2, 4, 5, 6, 8, 11 and 13 basic repeat units") (footnote omitted)
(D) uploaded by Beth A Sullivan, date unknown.
https://www.researchgate.net/fig ... eres_fig1_261222271
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板凳
 楼主| 发表于 11-24-2018 13:47:02 | 只看该作者
(c) Evgeny Krynetskiy, Beyond SNPs and CNV: Pharmacogenomics of Polymorphic Tandem Repeats. Journal of Pharmacogenomics & Pharmacoproteomics, 8: 170 (2017; review)
https://www.omicsonline.org/open ... 326&view=mobile

three consecutive paragraphs of Introduction (footnotes omitted):

" * * * Polymorphic Short Tandem Repeats (STR) emerged as a separate class of genetic mutations, which together with Single Nucleotide Polymorphisms (SNPs), Copy Number Variations (CNVs), and biallelic indels can explain variability in response to pharmacotherapy.

"Repetitive DNA sequences may comprise over two-thirds of the human genome. Depending on the length of the repeated motif, tandem repeats are categorized as microsatellites (short tandem repeats of DNA motifs 1 to 6 bp [base pair] long, or STR), minisatellites (tandem repeats of moderate motifs 10-100 bp long), and macrosatellites with motifs longer than 100 bp. In humans, STR makes up to 3% of the total genomic DNA which exceeds the protein coding part of the human genome.

"Depending on the search algorithm, there are approximately 700,000–1,000,000 STR loci with 2-6 bp long motifs in the human reference genome. Di- and tetra-nucleotide STR constitute about 75% of STR, with the remaining loci containing tri-, penta-, and hexa-nucleotide repeats. The overall STR density in the human genome is comparable across chromosomes (mean ± SD=13,613 ± 1,887 bp/Mb), with chromosome 19 showing the highest STR density (20,351 bp/Mb). Within genes, microsatellite repeats are non-randomly distributed across protein-coding sequences, untranslated regions (UTRs), and introns. In the coding regions of the genes, repeats predominantly have either trimeric or hexameric repeat unit, likely as a result of selection against frameshift mutations. * * *

* Quotation 1, applied to forensics, might have explained why Michael Sumpter's brother is excluded as the murder suspect.
* The term "macrosatellites" in quotation 2 is rarely use, which is rather referred to as alpha satellite. There is no need to read the rest.
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4#
 楼主| 发表于 11-24-2018 13:47:34 | 只看该作者
(d)
(i) Y-STR
https://en.wikipedia.org/wiki/Y-STR
(section 1 Nomenclature: "DYS is a variation on the jargon used in human autosomal STR testing where the second character is typically reserved for the chromosome number (eg D8S1179)")
(ii) Here is a graphic to help you conceptualize microsatellites.

Sequence-Tagged Sites (STS)
https://www.ncbi.nlm.nih.gov/probe/docs/techsts/
("Sequence-Tagged Site (STS) is a relatively short, easily PCR-amplified sequence (200 to 500 bp) which can be specifically amplified by PCR and detected in the presence of all other genomic sequences and whose location in the genome is mapped. * * * Microsatellites [(which is sectional heading):] * * * These polymorphisms are identified by constructing PCR primers for the DNA flanking the microsatellite region. The flanking regions tend to be conserved within the species, although sometimes they may also be conserved in higher taxonomic levels [graphic follows]")
(iii) Philip Ritter, The Y-Chromosome and Genetic Genealogy. Stanford University, 2005.
https://web.stanford.edu/~philr/Bachman/DNABachman3.html
("Markers. There are a number of different kinds of mutations (changes in the genetic code) that can occur when DNA is copied within a cell and passed on to the next generation. Short-tandem repeats (STR's), also known as microsatellites, are the markers tested in most genealogical y-chromosome studies. STR's occur at specific locations on the y-chromosome, which are often referred to as loci, and are given names such as 'DYS391.' STR's [plural form of STR] occur when short segments of DNA sequences get repeated over and over along a portion of a chromosome. For example, DYS391 consists of repeats of the base sequence -GATA-. Once an STR exists, it may change by adding or subtracting a repeat or two during the replication process. Estimates of the frequency of changes range from less than 2 mutations per 1000 generations to over 7 per 1000 generations for each STR, depending on which marker. Thus over a long period of time, individuals will tend to have at least some differences in the values (number of repeats) on the various STR markers on their y-chromosome. If you look at 25 markers, there is about a 50% chance you will find at least 1 mutation in 9-10 generations (or, counting both up and down from the common ancestor, between yourself and a 4th cousin). DYS391 can have values ranging from 7 to 14 repeats, with 10 and 11 being common in populations with European ancestry. There have been over 200 STR markers identified on the y-chromosome, but not all are variable enough for genealogical purposes. Testing companies currently test between 10 and 43 markers")

There is no need to read the rest. The press release of Middlesex district attorney did not say how many Y-STR markers/ loci it had tested.

(iv) Y-Chromosome STRs. National Institute of Standards and Technology, US Department of Commerce, undated.https://strbase.nist.gov/y_strs.htm
https://strbase.nist.gov/y_strs.htm

In the "General Information," view only the first two items:
• Y STR Positions along Chromosome
• Y Chromosome STR Fact Sheets (updated 1/08/2009)
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