Othram, a DNA forensics company I co-founded, has helped to solve another cold case.
Montana Girl, 5, Was Abducted Near Home and Found Dead in Drain — and Killer ID'd 46 Years Later
For 46 years, the family of Siobhan McGuinness waited to find out who killed the spunky 5-year-old back in 1974
On a frigid February afternoon in 1974, Siobhan McGuinness was walking the short distance home from a friend’s house in Missoula, Montana, when she vanished. Two days later, the 5-year-old’s body was found in a snow-covered drain culvert near the exit for Turah on I-90, just outside the city limits. She had been sexually assaulted. She also sustained trauma to her head and stab wounds to her chest, according to the FBI.
Detectives at the time searched tirelessly for the little girl’s killer, but came up empty. The case went cold for decades.
On Monday, authorities announced that after 46 years, the Missoula County Sheriff’s Office Cold Case Squad, detectives from the Missoula Police Department and others had finally identified the man who took the life of the spunky child who was always smiling. Richard William Davis was 32 when he was traveling through the area at the time of Siobhan’s murder, Missoula Police Chief Jason White said at a press conference on Monday. ...
Using DNA left behind at the crime scene, specialists at private technology company Othram Inc. were able to create a genealogical profile of the suspect, which led them to Davis, the company says in a press release.
See Othram: the future of DNA forensics
The existing FBI standard (CODIS) for DNA identification uses only 20 markers (STRs -- previously only 13 loci were used!). By contrast, genome wide sequencing can reliably call millions of genetic variants.
For the first time, the cost curves for these two methods have crossed: modern sequencing costs no more than extracting CODIS markers using the now ~30 year old technology.
What can you do with millions of genetic markers?
If you have contacts in law enforcement, please alert them to the potential of this new technology.1. Determine relatedness of two individuals with high precision. This allows detectives to immediately identify a relative (ranging from distant cousin to sibling or parent) of the source of the DNA sample, simply by scanning through large DNA databases. ...
Othram, a DNA forensics company I co-founded, has solved another cold case.
Carla Walker of Fort Worth TX was tortured, raped, and murdered in 1974. Finally the killer has been identified and arrested.
This was an open and high profile case just a few months ago. See this April 2020 episode of The DNA of Murder (Oxygen channel), hosted by Paul Holes, the detective who caught the Golden State Killer.
Who Killed Carla Walker? In 1974, 17-year-old Carla Walker’s reported abduction out of the arms of her boyfriend sent a Texas town on a massive manhunt. She was discovered murdered in a culvert three days later. Paul Holes interviews the only witness, Carla’s boyfriend.
Walker and her boyfriend, Western Hills High School football quarterback Rodney McCoy, attended a Valentine’s dance on Feb. 16, 1974. After the dance, they met up with friends and then stopped by a Fort Worth bowling alley.
McCoy has always maintained that a man approached the couple while they were sitting inside his car at the bowling alley parking lot and pointed a gun at him. He was beaten unconscious, and when he awoke, he found his cheerleader girlfriend missing.
See Othram: the future of DNA forensics
The existing FBI standard (CODIS) for DNA identification uses only 20 markers (STRs -- previously only 13 loci were used!). By contrast, genome wide sequencing can reliably call millions of genetic variants.
For the first time, the cost curves for these two methods have crossed: modern sequencing costs no more than extracting CODIS markers using the now ~30 year old technology.
What can you do with millions of genetic markers?
If you have contacts in law enforcement, please alert them to the potential of this new technology.1. Determine relatedness of two individuals with high precision. This allows detectives to immediately identify a relative (ranging from distant cousin to sibling or parent) of the source of the DNA sample, simply by scanning through large DNA databases. ...
Othram, a DNA forensics company I co-founded, continues to solve cold cases around the world.
Murder victim Rodney Peter Johnson was identified from a sample of only 0.2 nanograms of DNA (equivalent of 20 cells). Mr. Johnson had last been seen in 1987, when he was 25 years old. His body was discovered in 1994 by a fisherman in Lake Stickney, near Everett WA. It was badly decomposed and could not be identified.
The Johnson family has waited decades for closure. Press conference video.
See Othram: the future of DNA forensics
The existing FBI standard (CODIS) for DNA identification uses only 20 markers (STRs -- previously only 13 loci were used!). By contrast, genome wide sequencing can reliably call millions of genetic variants.
For the first time, the cost curves for these two methods have crossed: modern sequencing costs no more than extracting CODIS markers using the now ~30 year old technology.
What can you do with millions of genetic markers?
If you have contacts in law enforcement, please alert them to the potential of this new technology.1. Determine relatedness of two individuals with high precision. This allows detectives to immediately identify a relative (ranging from distant cousin to sibling or parent) of the source of the DNA sample, simply by scanning through large DNA databases. ...
Dr. John Hawks delivers a lecture on Ancient DNA & Human Origins at Michigan State University on October 4, 2018.
The rapidly changing field of ancient DNA has settled into a kind of normal science, as several teams of researchers have coalesced around a set of approaches to discover the genetic relationships among ancient peoples.
Hawks is the Vilas-Borghesi Distinguished Achievement Professor of Anthropology at the University of Wisconsin - Madison. He is an anthropologist and studies the bones and genes of ancient humans. He's worked on almost every part of our evolutionary story, from the very origin of our lineage among the apes up to the last 10,000 years of our history.
WIRED: ... "From just the fingerprint on your pen, we can sequence your genome and identify how you look," Venter explains. "It's good enough to pick someone out of a ten-person line-up and it's getting better all the time." These prediction algorithms were developed at Venter's latest venture, biosciences startup Human Longevity, Inc (HLi) by measuring 30,000 datapoints from across the faces of a thousand volunteers, then using machine learning to identify patterns between their facial morphology and their entire genetic code. "We could take foetal cells from a mother's bloodstream, sequence the genome and give her a picture of what her future child will look like at 18," he says.HLi's sequencing and phenotyping are done in San Diego, but the machine learning group hangs out at this third wave cafe in Mountain View :-)
High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects
Nature 529, 490–495 (28 January 2016) doi:10.1038/nature16526
CRISPR–Cas9 nucleases are widely used for genome editing but can induce unwanted off-target mutations. Existing strategies for reducing genome-wide off-target effects of the widely used Streptococcus pyogenes Cas9 (SpCas9) are imperfect, possessing only partial or unproven efficacies and other limitations that constrain their use. Here we describe SpCas9-HF1, a high-fidelity variant harbouring alterations designed to reduce non-specific DNA contacts. SpCas9-HF1 retains on-target activities comparable to wild-type SpCas9 with >85% of single-guide RNAs (sgRNAs) tested in human cells. Notably, with sgRNAs targeted to standard non-repetitive sequences, SpCas9-HF1 rendered all or nearly all off-target events undetectable by genome-wide break capture and targeted sequencing methods. Even for atypical, repetitive target sites, the vast majority of off-target mutations induced by wild-type SpCas9 were not detected with SpCas9-HF1. With its exceptional precision, SpCas9-HF1 provides an alternative to wild-type SpCas9 for research and therapeutic applications. More broadly, our results suggest a general strategy for optimizing genome-wide specificities of other CRISPR-RNA-guided nucleases.
Rationally engineered Cas9 nucleases with improved specificity
Science 01 Jan 2016: Vol. 351, Issue 6268, pp. 84-88
DOI: 10.1126/science.aad5227
The RNA-guided endonuclease Cas9 is a versatile genome-editing tool with a broad range of applications from therapeutics to functional annotation of genes. Cas9 creates double-strand breaks (DSBs) at targeted genomic loci complementary to a short RNA guide. However, Cas9 can cleave off-target sites that are not fully complementary to the guide, which poses a major challenge for genome editing. Here, we use structure-guided protein engineering to improve the specificity of Streptococcus pyogenes Cas9 (SpCas9). Using targeted deep sequencing and unbiased whole-genome off-target analysis to assess Cas9-mediated DNA cleavage in human cells, we demonstrate that “enhanced specificity” SpCas9 (eSpCas9) variants reduce off-target effects and maintain robust on-target cleavage. Thus, eSpCas9 could be broadly useful for genome-editing applications requiring a high level of specificity.
Eight thousand years of natural selection in EuropeFrom the paper:
http://dx.doi.org/10.1101/016477
The arrival of farming in Europe beginning around 8,500 years ago required adaptation to new environments, pathogens, diets, and social organizations. While evidence of natural selection can be revealed by studying patterns of genetic variation in present-day people, these pattern are only indirect echoes of past events, and provide little information about where and when selection occurred. Ancient DNA makes it possible to examine populations as they were before, during and after adaptation events, and thus to reveal the tempo and mode of selection. Here we report the first genome-wide scan for selection using ancient DNA, based on 83 human samples from Holocene Europe analyzed at over 300,000 positions. We find five genome-wide signals of selection, at loci associated with diet and pigmentation. Surprisingly in light of suggestions of selection on immune traits associated with the advent of agriculture and denser living conditions, we find no strong sweeps associated with immunological phenotypes. We also report a scan for selection for complex traits, and find two signals of selection on height: for short stature in Iberia after the arrival of agriculture, and for tall stature on the Pontic-Caspian steppe earlier than 5,000 years ago. A surprise is that in Scandinavian hunter-gatherers living around 8,000 years ago, there is a high frequency of the derived allele at the EDAR gene that is the strongest known signal of selection in East Asians and that is thought to have arisen in East Asia. These results document the power of ancient DNA to reveal features of past adaptation that could not be understood from analyses of present-day people.
... We also tested for selection on complex traits, which are controlled by many genetic variants, each with a weak effect. Under the pressure of natural selection, these variants are expected to experience small but correlated directional shifts, rather than any single variant changing dramatically in frequency, and recent studies have argued that this may be a predominant mode of natural selection in humans40. The best documented example of this process in humans is height, which has been shown to have been under recent selection in Europe41. At alleles known from GWAS to affect height, northern Europeans have, on average, a significantly higher probability of carrying the height-increasing allele than southern Europeans, which could either reflect selection for increased height in the ancestry of northern Europeans or decreased height in the ancestry of southern Europeans. To test for this signal in our data, we used a statistic that tests whether trait-affecting alleles are more differentiated than randomly sampled alleles, in a way that is coordinated across all alleles consistent with directional selection42. We applied the test to all populations together, as well as to pairs of populations in order to localize the signal (Figure 3, Extended Data Figure 5, Methods).
We detect a significant signal of directional selection on height in Europe (p=0.002), and our ancient DNA data allows us to determine when this occurred and also to determine the direction of selection. Both the Iberian Early Neolithic and Middle Neolithic samples show evidence of selection for decreased height relative to present-day European Americans (Figure 3A; p=0.002 and p < 0.0001, respectively). Comparing populations that existed at the same time (Figure 3B), there is a significant signal of selection between central European and Iberian populations in each of the Early Neolithic, Middle Neolithic and present-day periods (p=0.011, 0.012 and 0.004, respectively). Therefore, the selective gradient in height in Europe has existed for the past 8,000 years. This gradient was established in the Early Neolithic, increased into the Middle Neolithic and decreased at some point thereafter. Since we detect no significant evidence of selection or change in genetic height among Northern European populations, our results further suggest that selection operated mainly on Southern rather than Northern European populations. There is another possible signal in the Yamnaya, related to people who migrated into central Europe beginning at least 4,800 years ago and who contributed about half the ancestry of northern Europeans today9 . The Yamnaya have the greatest predicted genetic height of any population, and the difference between Yamnaya and the Iberian Middle Neolithic is the greatest observed in our data. ...
NYTimes: Is Most of Our DNA Garbage?
... Rinn studies RNA, but not the RNA that our cells use as a template for making proteins. Scientists have long known that the human genome contains some genes for other types of RNA: strands of bases that carry out other jobs in the cell, like helping to weld together the building blocks of proteins. In the early 2000s, Rinn and other scientists discovered that human cells were reading thousands of segments of their DNA, not just the coding parts, and producing RNA molecules in the process. They wondered whether these RNA molecules could be serving some vital function.
... In December 2013, Rinn and his colleagues published the first results of their search: three potential new genes for RNA that appear to be essential for a mouse’s survival. To investigate each potential gene, the scientists removed one of the two copies in mice. When the mice mated, some of their embryos ended up with two copies of the gene, some with one and some with none. If these mice lacked any of these three pieces of DNA, they died in utero or shortly after birth. “You take away a piece of junk DNA, and the mouse dies,” Rinn said. “If you can come up with a criticism of that, go ahead. But I’m pretty satisfied. I’ve found a new piece of the genome that’s required for life.”
... To some biologists, discoveries like Rinn’s hint at a hidden treasure house in our genome. Because a few of these RNA molecules have turned out to be so crucial, they think, the rest of the noncoding genome must be crammed with riches. But to Gregory and others, that is a blinkered optimism worthy of Dr. Pangloss. They, by contrast, are deeply pessimistic about where this research will lead. Most of the RNA molecules that our cells make will probably not turn out to perform the sort of essential functions that hotair and firre do. Instead, they are nothing more than what happens when RNA-making proteins bump into junk DNA from time to time.
... One news release from an N.I.H. project declared, “Much of what has been called ‘junk DNA’ in the human genome is actually a massive control panel with millions of switches regulating the activity of our genes.” Researchers like Gregory consider this sort of rhetoric to be leaping far beyond the actual evidence.
... Over millions of years, essential genes haven’t changed very much, while junk DNA has picked up many harmless mutations. Scientists at the University of Oxford have measured evolutionary change over the past 100 million years at every spot in the human genome. “I can today say, hand on my heart, that 8 percent, plus or minus 1 percent, is what I would consider functional,” Chris Ponting, an author of the study, says. And the other 92 percent? “It doesn’t seem to matter that much,” he says. ...
Large multiallelic copy number variations in humans
Nature Genetics (2015) doi:10.1038/ng.3200
Thousands of genomic segments appear to be present in widely varying copy numbers in different human genomes. We developed ways to use increasingly abundant whole-genome sequence data to identify the copy numbers, alleles and haplotypes present at most large multiallelic CNVs (mCNVs). We analyzed 849 genomes sequenced by the 1000 Genomes Project to identify most large (>5-kb) mCNVs, including 3878 duplications, of which 1356 appear to have 3 or more segregating alleles. We find that mCNVs give rise to most human variation in gene dosage—seven times the combined contribution of deletions and biallelic duplications— and that this variation in gene dosage generates abundant variation in gene expression. We describe ‘runaway duplication haplotypes’ in which genes, including HPR and ORM1, have mutated to high copy number on specific haplotypes. We also describe partially successful initial strategies for analyzing mCNVs via imputation and provide an initial data resource to support such analyses.
Nature: ... Although the average level of population differentiation is low (at sites genotyped in all populations the mean value of Wright’s Fst is 0.071 between CEU and YRI, 0.083 between YRI and CHB+JPT, and 0.052 between CHB+JPT and CEU), we find several hundred thousand SNPs with large allele frequency differences in each population comparison (Fig. 5c). As seen in previous studies4, 37, the most highly differentiated sites were enriched for non-synonymous variants, indicative of the action of local adaptation. The completeness of common variant discovery in the low-coverage resource enables new perspectives in the search for local adaptation. First, it provides a more comprehensive catalogue of fixed differences between populations, of which there are very few: two between CEU and CHB+JPT (including the A111T missense variant in SLC24A5 (ref. 38) contributing to light skin colour), four between CEU and YRI (including the −46 GATA box null mutation upstream of DARC39, the Duffy O allele leading to Plasmodium vivax malaria resistance) and 72 between CHB+JPT and YRI (including 24 around the exocyst complex component gene EXOC6B); see Supplementary Table 7 for a complete list. Second, it provides new candidates for selected variants, genes and pathways. For example, we identified 139 non-synonymous variants showing large allele frequency differences (at least 0.8) between populations (Supplementary Table 8), including at least two genes involved in meiotic recombination—FANCA (ninth most extreme non-synonymous SNP in CEU versus CHB+JPT) and TEX15 (thirteenth most extreme non-synonymous SNP in CEU versus YRI, and twenty-sixth most extreme non-synonymous SNP in CHB+JPT versus YRI). Because we are finding almost all common variants in each population, these lists should contain the vast majority of the near fixed differences among these populations. Finally, it improves the fine mapping of selective sweeps (Supplementary Fig. 14) and analysis of the dynamics of location adaptation. For example, we find that the signal of population differentiation around high Fst genic SNPs drops by half within, on average, less than 0.05 cM (typically 30–50 kb; Fig. 5d). Furthermore, 51% of such variants are polymorphic in both populations. These observations indicate that much local adaptation has occurred by selection acting on existing variation rather than new mutation.
We estimated a fine-scale genetic map from the phased low-coverage genotypes. Recombination hotspots were narrower than previously estimated4 (mean hotspot width of 2.3 kb compared to 5.5 kb in HapMap II; Fig. 6a), although, unexpectedly, the estimated average peak recombination rate in hotspots is lower in YRI (13 cM Mb−1) than in CEU and CHB+JPT (20 cM Mb−1). In addition, crossover activity is less concentrated in the genome in YRI, with 70% of recombination occurring in 10% of the sequence rather than 80% of the recombination for CEU and CHB+JPT (Fig. 6b). A possible biological basis for these differences is that PRDM9, which binds a DNA motif strongly enriched in hotspots and influences the activity of LD-defined hotspots40, 41, 42, 43, shows length variation in its DNA-binding zinc fingers within populations, and substantial differentiation between African and non-African populations, with a greater allelic diversity in Africa43. This could mean greater diversity of hotspot locations within Africa and therefore a less concentrated picture in this data set of recombination and lower usage of LD-defined hotspots (which require evidence in at least two populations and therefore will not reflect hotspots present only in Africa).
OG-500 DNA Tube
Overview
The OG-500 DNA Collection Kit provides an all-in-one system for the collection, stabilization, transportation and purification of DNA from saliva.
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It was clear to me that I was faced with a novelty: enormous ambition and aggressiveness, coupled with an almost complete ignorance of, and a contempt for, chemistry, that most real of exact sciences - a contempt that was later to have a nefarious influence on the development of "molecular biology." Thinking of the many sweaty years of making preparations of nucleic acids and of the innumerable hours spent on analyzing them, I could not help being baffled. I am sure that, had I had more contact with, for instance, theoretical physicists, my astonishment would have been less great. In any event, there they were, speculating, pondering, angling for information. ...Thanks for digging around down there -- what did you find, again? Great! I've got more horsepower, so I'll just connect the dots for you now... :-) From Wikipedia on Crick:
Crick had to adjust from the "elegance and deep simplicity" of physics to the "elaborate chemical mechanisms that natural selection had evolved over billions of years." He described this transition as, "almost as if one had to be born again." According to Crick, the experience of learning physics had taught him something important—hubris—and the conviction that since physics was already a success, great advances should also be possible in other sciences such as biology. Crick felt that this attitude encouraged him to be more daring than typical biologists who tended to concern themselves with the daunting problems of biology and not the past successes of physics.