Category Archives: Transhuman News

The decoding of the genome was a sensation, although the announcement by Craig Venter on April 6, 2000, was somewhat premature. It actually took another year before the Human Genome Project (HGP), which was in competition with Venter, published its peer-reviewed research results in the scientific journal Science and Nature on February 15, 2001.

Battle for first place

The decoding of the genome was a race for scientific fame between the HGP, which is government-funded by the US, and Venter with his private company Celera Genomics. The government researchers lagged somewhat behind Celera Genomics in their work. By April 2000, they had been able to decode only 54% of the human genome.

The genome is made up of the genetic storage material deoxyribonucleic acid (DNA). It contains all hereditary information of life.

Read more:Blood test detects more than 50 types of cancer

Craig Venter 1998 in the laboratory of his company Celera Genomics. Venter invented the shotgun sequencing method.

Going after the genetic material with a shotgun

Venter used a different sequencing method than the HGP researchers: namely, the so-called shotgun method that he developed. In this method, the individual DNA fragments are generated randomly. This is similar to shooting at the long chain with a shotgun and then looking at and reading out the fragments individually.

However, Venter also used HGP data to achieve his goal. And that was an ambitious one: The human genome consists of 3.2 billion base pairs the letters of life, so to speak. Finding them all was a mammoth task for him and the competing researchers. But the design of this genetic chain is actually quite simple.

It consists of a sequence of only four different building blocks: the DNA bases cytosine (C), guanine (G), adenine (A) and thymine (T). It is the sequence of these bases that determines our eye or hair color or whether we have any hereditary diseases.

Read more:Stone-Age 'chewing gum' reveals human DNA

Many doors leading nowhere

Only a few sections of the entire genome are the genes that contain important instructions for building blocks of life such as proteins. "According to current knowledge, however, a large proportion of DNA is an evolutionary remnant and has no function whatsoever. This makes it clear that although the door to the code of life has been opened, countless new doors are hidden behind it," writes chemist Friederike Fehr from the Max Planck Institute for Dynamics and Self-Organization in Gttingen.

Many genes that were discovered in the genome sequence had been unknown until then. "So the effects or tasks associated with them must also be researched. The sequence of letters alone is of limited help in this regard," Fehr writes.

Long road to medical applications

It was only with the completion of sequencing that the project of decoding the human genome could bear practical fruit. Although Venter published his own personal genome in the scientific journal PLoS Biology in 2007, this, too, was of rather symbolic importance. Gene sequencing in itself was only a first step toward a fundamental change in our medicine.

Scientists still had to research and assign the respective functions of the individual building blocks of the genome, i.e. find out which building block is responsible for what. They did this with the help of mice. Their genome is largely identical to that of humans and thus provided a basis for understanding the functions of human genes.

Experts believe that it could take dozens, if not hundreds, of years to really understand the human genome.

Read more:Who's the daddy: Does it really matter where your DNA comes from?

What do we get out of this?

The genomes of two people differ. These differences are the basis for the genetic predisposition to certain diseases.

Increasingly, genetic tests are being offered that enable experts to identify some of these predispositions and thus determine whether or not a person carries an increased risk of disease. A saliva sample is sufficient for this.

The most important thing in all these tests is to interpret the results correctly, for example, to determine if there is the disposition for Alzheimer's or diabetes.

With the help of genome research, it is now possible to identify various gene functions. This in turn helps doctors to treat certain diseases, including in children with an immune deficiency that is hereditary. Doctors can even implant new genes into these children to treat the disease.

Breast and ovarian cancer become apparent in the alterations of two genes (BRCA1 and BRCA2). A genetic risk for a tumor disease can be detected only in a few cases by genetic analysis.

There is still much to be done

The human genome consists of roughly22,500genes. Researchers around the world were astonished at this result as, believe it or not, a water flea has 30,907.

How complex a living being is, therefore, not dependent only on the number of genes. US President Bill Clinton said on April 6, 2000: "Now we are learning the language with which God created life." We now know that we still need a lot more vocabulary before we master that language.

This article has been edited and correctedsince it's first publication on 5 April 2020

Read more:Barley geneticists toast to future of better beer

In 1891, a Croatian born, Argentine criminologist, Juan Vucetich, started building up the first modern-style fingerprint archive. Since then, fingerprints have become one of the main forms of evidence used to convict criminals. Here, a police officer spreads dust on the lock of a burglarized apartment. Fingerprints become visible.

He uses an adhesive film to capture the fingerprint. Then he glues it to a piece of paper. In the past, comparing fingerprints was a painstaking affair. Officers had to compare fingerprints found at the scene of a crime, one-by-one, with those of possible suspects. These days computers do the job.

Taking fingerprints used to be a messy affair - with ink and dirty hands. These days scanners have replaced the inky mess. And the data can immediately be sent to a database and turned into biometrical data.

The computer identifies typical spots within the ridge patterns of the fingerprint. These include forks in the lines, spots and the location of the center of the print. Fingerprints are never the same between two people - not even with identical twins.

No chance! Here, officials use fingerprint scanners during an election in Nigeria. It's how they make sure the people voting are registered voters and that they only vote once.

This is an important question for officials who have to decide about the refugee or asylum status of applicants. In the European Union all migrants are supposed to have their fingerprints taken at the first point of entry - provided, of course, the local police officers are equipped with the scanners.

Many smartphones now come with fingerprint recognition software, such as the iPhone's Touch-ID. The owner of the phone unlocks it with his fingerprint. If someone else finds or steals the phone, they have no way of getting at any encrypted data within.

This is an Automatic Teller Machine (ATM) in the Scottish town of Dundee. Customers wanting to withdraw money need to show biometric proof of identity - in the form of a fingerprint. Not good news for pickpockets.

Since 2005, German passports, and many other passports, contain a digital fingerprint as part of the biometric information stored on a RFID (radio-frequency controlled ID) chip. Other information on the chip includes a biometric passport photo. The facial image is similar to fingerprints: no two images are alike.

Facial recognition software, which uses biometrics, is well advanced. It is possible to identify suspects within large crowds, with surveillance cameras. Also internet services and private computer owners are increasingly making use of facial recognition software to sort holiday pictures and tagging them to names.

Alec Jeffreys discovered DNA-fingerprinting almost accidentally in 1984 during research at the University of Leicester. He identified a specific pattern on DNA segments, which were different for every human. He created a picture, which looks like a barcode at the supermarket.

Germany's Federal Criminal Police Office (BKA) started storing such barcodes in a federal database in 1998. Investigators have since solved more than 18,000 crimes, using genetic fingerprints.

It's not just criminals who get identified. Many innocent people can be cleared of criminal charges through good identification. For some, technology has saved their lives. Kirk Bloodsworth spent almost nine years on death row. The US Innocence Project has proved the false incarceration of more than 100 people using DNA evidence.

The first big test for DNA-fingerprinting came with the mass murder of Srebrenica. Bodies, exhumed from mass graves, were systematically identified using DNA techniques. They were then reburied by their loved ones. Here, five year old Ema Hasanovic pays last respects to her uncle. More than 6,000 victims of the massacre - mostly men - were identified using DNA-fingerprinting.

You may be surprised, but there's biometric information in sounds and other digital data. Voice recognition software can, for instance, identify people making threatening phone calls - the human voice is also unique. And don't forget: we leave all kinds of digital traces on the internet, which hold clues to who we really are.

Author: Fabian Schmidt

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Craig Venter: 20 years of decoding the human genome - DW (English)

Two teams of scientists in Italy have collaborated on a project that further analyzed the SARS-CoV-2 genome from locally acquired samples. The analysis of the samples via next-generation sequencing (NGS) reveals a specific level of genetic variability that implies the SARS-CoV-2 genome is stable.The results are useful in the development of a safe and effective vaccine against SARS-CoV-2, as the more stable the virus's genome, the greater likelihood that a vaccine will be effective globally across populations.Technology Networks spoke with Professor Stefano Menzo, virologist, and Dr Valerio Onofri, geneticist, affiliates of the Department of Excellence of Biomedical Science and Public Health, Marche Polytechnic University in Ancona, to learn more about the findings.Molly Campbell (MC): For our readers that may be unfamiliar, please can you explain how next-generation sequencing (NGS) is utilized to explore the genome of the SARS-CoV-2 virus?Valerio Onofri (VO): NGS is a high-throughput method to sequence DNA or RNA. Unlike the classic Sanger sequencing method, NGS provides millions to billions of short nucleotide sequence reads in just a few hours and at lower costs. This method is routinely used to find pathogenetic variants that cause inherited disease or cancer. It is also useful to discover the sequence of an unknown viral, prokaryote or eukaryote genome.When a reference sequence becomes available, NGS labs can sequence a clinical or population sample, align the new sequence to the reference and annotate the differences to determine whether mutations have occurred. We are doing this work now to better understand the SARS-CoV-2 virus. The virus was first sequenced in December 2019 and in February 2020 in Wuhan, China where it originated. When the pandemic spread, many labs like ours began sequencing virus samples from local patients to detect variants and study their significance. NGS provides both fast whole genome sequencing and, thanks to sequencing redundancy, quasispecies analysis (analysis of both major and minor variants).MC: Please can you tell us about The Ion AmpliSeq SARS-COV-2 Research Panel?VO: This panel was designed by Thermo Fisher Scientific to provide an efficient, high-throughput workflow for analyzing the entire SARS-CoV-2 genome on the Ion Torrent platform. Based on the targeted approach by amplicons method, it consists of about 250 PCR cycles to amplify the full SARS-COV-2 genome. Drawing on our expertise from routinely using this method for forensic and medical genetics, we helped Thermo Fisher validate the panel in virus isolates as well as throat/nasal swabs. It is now widely available for NGS-based research to better understand COVID-19.MC: What have your analyses so far revealed about the genetic stability of the SARS-CoV-2 virus?Stefano Menzo (SM): So far, SARS-CoV-2 appears to be a relatively stable virus, meaning it does not display many variants in the quasispecies, compared to other known RNA viruses such as HCV or HIV.MC: What does the SARS-CoV-2 genome reveal about the evolutionary path of the coronavirus?SM: More sequencing of full-length genomes throughout the world will be necessary to better answer this question. For now, we can say the virus has started differentiating in the human population from a common ancestor at a slow/moderate pace.MC: How can this data be utilized in the development of preventatives/ therapeutics against the COVID-19 outbreak?SM: Any vaccine will work best throughout the world if the virus is relatively confined geographically to limit the generation of escape mutants. The same is true for any antiviral treatment.MC: What are your next steps in this research space?SM: We will continue to investigate the viruss evolution by sequencing samples from patients with different clinical outcomes.Professor Stefano Menzo, virologist, and Dr. Valerio Onofri, geneticist, affiliates of the Department of Excellence of Biomedical Science and Public Health, Marche Polytechnic University in Ancona, were speaking to Molly Campbell, Science Writer, Technology Networks.

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Further Analysis of SARS-CoV-2 Genome Suggests It Is Stable - Technology Networks

President Donald Trump lashed out at The New York Times on Saturday.

So now the Fake News The New York Times is tracing the CoronaVirus origins back to Europe, NOT China. This is a first! I wonder where (sic) the Failing New York Times got for this one? Are there any NAMED sources? Trump wondered.

However, the reporting from The Times was not based on anonymous sources.

New research indicates that the coronavirus began to circulate in the New York area by mid-February, weeks before the first confirmed case, and that travelers brought in the virus mainly from Europe, not Asia, The Times reported on Wednesday.

The story cited now research by geneticists at the Icahn School of Medicine at Mount Sinai and the N.Y.U. Grossman School of Medicine.

Both teams analyzed genomes from coronaviruses taken from New Yorkers starting in mid-March, the newspaper noted. The research revealed a previously hidden spread of the virus that might have been detected if aggressive testing programs had been put in place.

Trump appeared bored on Saturday as he went for his second weekend without playing golf.

Trump spent the early evening praising a West Virginia resident for comments made when they called in to C-SPAN and complaining about Fox News hours before a Fox News interview.

https://twitter.com/realDonaldTrump/status/1249101675509370882

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Trump wonders if COVID-19 genomes gave fake quotes to the NYT in bizarre Saturday outburst - Raw Story

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Just two weeks after developing a test for COVID-19, Gundersen Medical Foundation researchers have successfully sequenced the complete viral genomes of the virus, an achievement that will help researchers understand its origins and evolution during spread.

The Gundersen Medical Foundation cancer research team, directed by Dr. Paraic Kenny, has been utilizing the Foundations cancer genome sequencing equipment to examine COVID-19 infections in La Crosse County patients and how they correlate with the global pandemic.

To conduct the research, Kenny and his team secured Institutional Review Board approval to use specimens, remaining after the conducting of standard COVID-19 testing, from six of the La Crosse Countys earliest cases of the virus.

At the most basic level, the virus makes occasional spelling mistakes when it copies its genome during infection and these mutations are faithfully carried in all subsequent infections by that particular virus, Kenny says. By sequencing the whole viral genome, we have been able to map the different COVID-19 strains currently in La Crosse County. This allows us to go far beyond positive and negative test results to better understand how the virus spreads within our community and health-care system.

Through its local lab, Kennys research team has been able to document the independent appearance of COVID-19 strains in the Coulee Region, discovering several of the viruses sequenced share molecular fingerprints with viruses that traveled directly from China to Washington state, as well as strains that circulated about a month ago in France and one sub-strain present in community spread.

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Gundersen researchers sequence genomes of COVID-19, results help with tracking and possibly mitigating spread - La Crosse Tribune

Investigators have identified genomic alterations that appear to be associated with prognosis in men with metastatic castration-sensitive prostate cancer (mCSPC).

Astudy of 424 patients with mCSPC treated at a tertiary care center revealedthat alterations in the androgen receptor (AR), TP53, cell-cycle, MYC oncogenicsignaling pathways occur more commonly in tumors with worse overall survivaland decreased time to castration-resistant disease, whereas alterations in theSPOP and MNT pathways occur more frequently in tumors with a better prognosis,according to findings published in ClinicalCancer Research.

Thegenomics of metastatic castration-sensitive prostate cancer have not been wellcharacterized in the literature, but it is now clear that upfront treatmentintensification with taxanes or next-generation AR-directed therapies offerbenefit in the overall patient population, said the studys co-senior authorWassim Abida, MD, a medical oncologist at Memorial Sloan Kettering CancerCenter in New York. The question remains whether treatment selection ortargeted therapies can be employed based on genomic characteristics.

Theassociation between alterations in cell-cycle genes and TP53 and MYC pathwaygenes and worse outcomes may pave the way for targeted therapy in thesehigher-risk groups, Dr Abida said.

Thestudy compared genomic alterations according to clinical phenotypes: high- vslow-volume disease and de novo vsmetastatic recurrence. Of the 424 patients in the study, 213 men (50%) hadhigh-volume disease (4 or more bone metastases or visceral metastases) and 211(50%) had low-volume disease; 65% had de novometastases and 35% had metastatic recurrence. At the time of sample collection, patients had a medianage of 66 years. The investigators conducted gene sequencing from May 2015 to September2018.

High- vs low-volume disease

Inadjusted analyses, men with higher-volume disease had significant 1.8- and3.7-fold increased risks of castration-resistant disease and death,respectively, compared with men who had low-volume disease. Tumor specimensfrom men with high-volume disease had more copy number alterations.

Amongmen with high-volume disease, the highest-ranking pathways were the NOTCH,cell-cycle, and epigenetic modifiers pathways.

Althoughthe prevalence of CDK12 alterations differed between patients with de novo metastatic and those with metastaticrecurrences, the groups had similar prognoses. I was actually surprised therewere not more dramatic genomic differences between de novo and relapsed disease, said study co-senior author PhilipKantoff, MD, a medical oncologist and Chair of the Department of Medicine atMemorial Sloan Kettering Cancer Center in New York.

Afteradjusting for disease volume and other genomic pathways, the researchers foundthat the rates of castration resistance differed by 1.5-fold and up to 5-fold accordingto alterations in the AR, SPOP (inverse), TP53, cell-cycle, WNT (inverse), andMYC pathways. Overall survival (OS) rates varied from 2- to 4-fold according toalterations in the AR, SPOP (inverse), WNT (inverse), and cell-cycle pathways.PI3K pathway alterations were not associated with prognosis.

Docetaxeland next-generation AR axis-directed therapies have been shown to prolong OS, butit remains uncertain which patients benefit the most from intensifiedtherapies. We did not find any obvious genomic reason to explain thedifferences in docetaxel sensitivity between high- and low-volume disease, DrKantoff said.

Theauthors pointed out that genomic landscape studies of tumor DNA profiling inprostate cancer in general have excluded metastatic castration-sensitive tumors.Instead, most studies have focus on localized disease or metastaticcastration-resistant disease.

DrAbida and his colleagues acknowledged that their study has inherent biases becauseit was hospital based and enrolled patients at an academic referral center.

Moleculardeterminants of castration resistance or survival in patients with mHSPC have beenunclear, but the new study sheds new light on molecular alterations associatedwith poor outcomes in men with mHSPC, particularly alterations in the AR, cellcycle genes, MYC, and TP53 genes, said Joshi Alumkal, MD, the Leader of theProstate/Genitourinary Medical Oncology Section and Associate Division Chieffor Basic Research in the Hematology-Oncology Division at the University ofMichigan School of Medicine.

Severalrandomized phase 3 clinical trials now show a benefit of escalating treatmentin men with mHSPC by adding novel AR-targeting agents or chemotherapy plusmedical castration versus medical castration alone, Dr Alumkal said. Whetherthe addition of any of these specific agents to medical castration isassociated with improved outcomes in patients with poor-risk molecularalterations identified by the new study is a critical next question, he said.

Urologiconcologist James Mohler, MD, Senior Vice President for Translational Researchat Roswell Park Comprehensive Cancer Center in Buffalo, New York, said the new study found relativelysmall differences among the clinical phenotypes, but that is not surprisingbecause the temporal differences in the evolution of tumor biology occur overlong periods of time, much of which precedes clinical presentation. The hazardratios for association between mutational analysis and oncologic outcome insome cases were statistically significant, but are so small as to not beclinically significant. Part of the reason for this may be that prostatecancer, once metastatic, is so complex that no single mutation or single genepathway is driving growth and hence targetable at a high rate beyond the long provenbenefit from androgen deprivation therapy, Dr Mohler said.

Theresults reported by these authors may be disappointing to many clinicians, butare important because they represent a comprehensive analysis of mCSPC. Theauthors appropriately acknowledge that better tumor sampling and morecomprehensive genetic analysis and larger numbers of patients may be requiredto find any benefit to genomic or somatic sequencing, Dr Mohler said. I amafraid that these limitations are not just of their work but a biologicallimitation of aggressive prostate cancer, which makes improving treatment ofadvanced prostate cancer in an individual patient extremely challenging.

Reference

Stopsack KH, Nandakumar S, Wibmer AG, et al. Oncogenic genomic alterations, clinical phenotypes, and outcomes in metastatic castration-sensitive prostate cancer [published online March 27, 2020]. Clin Cancer Res. doi: 10.1158/1078-0432.CCR-20-0168

See the rest here:
Genomic Alterations Linked to Outcomes in mCSPC - Renal and Urology News

In this episode of Genetics Unzipped, recorded at the recent Festival of Genomics in London, Kat Arney finds out why its so important to make sure that both academic and commercial research studies are done with rather than on participants.

Research into genetic conditions relies on information from patients and their families, whether thats detailed health records or genomic data. As the tools and techniques for DNA and data analysis become cheaper and more organisations get in on this fast-growing field, its vital to make sure that the most valuable research resource human lives doesnt get overlooked in the rush.

Fiona Copelandis the chair of a support group for UK families affected by primary ciliary dyskinesia or PCD a rare genetic condition that affects the lungs and is the mother of two adult sons with the condition. Shes spent many years acting as a patient representative, engaging with academic and industry scientists looking to involve PCD patients in research into understanding and treating the condition. She explains what her role involves and shares her advice for how researchers can engage and involve patient groups more effectively. Her top tip? Dont make children cry!

Next Arney speaks with Patrick Short. Hes the CEO of Sano Genetics a Cambridge-based startup that aims to connect researchers with patients who want to take part in genomic research. While some companies using patients in research have come under scrutiny for poor handling of data and ethical compliance, Short is keen to help organizations do better and drive change in the fast-growing commercial genomics sector.

Finally, we hear from Shelley Simmonds, a disability rights campaigner and rare disease advocate whose son Fraser was initially given a diagnosis of Duchenne Muscular Dystrophy as a baby. When Fraser didnt seem to be progressing as might be expected for a child with the disease, she and her family got involved in Genomics Englands 100,000 Genomes Project in search of clarity but things turned out not to be quite so simple. Shelley talks what happens when the question Whats wrong with my child? has no answer.

Full transcript, links and references available online atGeneticsUnzipped.com

Genetics Unzippedis the podcast from the UKGenetics Society,presented by award-winning science communicator and biologistKat Arneyand produced byFirst Create the Media.Follow Kat on Twitter@Kat_Arney,Genetics Unzipped@geneticsunzip,and the Genetics Society at@GenSocUK

Listen to Genetics Unzipped onApple Podcasts(iTunes)Google Play,Spotify,orwherever you get your podcasts

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Podcast: Nothing about me without meThe importance of involving patients in genomic research - Genetic Literacy Project