Thirty years later, HudsonAlpha investigators reflect on the Human Genome Project

Today, genomic testing is so common it can be initiated from the comfort of your own home. It’s easy to forget that the human genome sequence was first determined less than two decades ago. The monumental task of creating the first human reference genome came from a 13-year international labor of love.

“Thinking about the entire genome at once instead of one gene at a time changed biology forever,” said HudsonAlpha co-founder Jim Hudson.

October marked the 30-year anniversary of the inception of the Human Genome Project. HudsonAlpha faculty investigators recently reflected on the monumental accomplishment and lasting legacy of the project.

Sequencing the whole genome

In the mid-1980s, a group of leaders in the human genetics field at a scientific meeting in Alta, Utah, were discussing how to determine the rate of mutation in a given person’s DNA. Rick Myers is now president, science director and Loya Chair in Genomics at the HudsonAlpha Institute for Biotechnology, but during the conference was a postdoctoral fellow at Harvard University. He vividly recalls this discussion because it highlighted the wonder and imagination from which the Human Genome Project was born.

The group concluded that the mutation rates were so low that they would have to sequence the entire human genome to figure it out, a feat which seemed so impossible at the time that the members of the summit laughed together at the idea. However, one year later, the Department of Energy proposed a dedicated project that would change the scientific community forever.

What is the Human Genome Project?

The Human Genome Project was an international, collaborative research effort to sequence the entire human genome and identify human genes. Beginning on Oct. 1, 1990, more than 2,800 researchers at 20 institutions across the United States, the United Kingdom, France, Germany, Japan and China began working on the consortium. It was a collaborative project that would not have been completed as quickly or efficiently had it not been for the participation of so many researchers. The full sequence was completed and published two years ahead of schedule in April 2003.

Sequencing the human genome showed that the 3.1 billion nucleotides in the human genome make up only about 20,000-25,000 human protein-coding genes. In addition to the human genome sequence, the project sequenced the genomes of several model organisms and developed new technologies to study whole genomes. Whole genome sequencing technology opened the door for sequencing any biological system on the planet, which drastically changed researchers’ ability to gain genomic knowledge and apply it in wise ways.

“We have millions of times more data about the human genome now, and the Human Genome Project made that possible,” said Myers. “We can now explore and learn things much faster and much more thoroughly than we could before. And the quicker you learn something, the quicker you can do something about it.

“For example, Gleevec, the groundbreaking drug used to treat chronic myelogenous leukemia and other cancers, is a notable success in which genomic understanding led to the rapid discovery of a protein responsible for the disease and the consequent development and FDA approval of a drug to block it,” Myers said. “This is only one of the many examples of diseases we are now more informed about because of the legacy of the Human Genome Project.”

HudsonAlpha’s connections to the project

Myers led a team at the Stanford Human Genome Center that, along with the Joint Genome Institute in Walnut Creek, California, contributed more than 10% of the data in the public Human Genome Project’s efforts. Initially, a few scientists, including some prominent ones, were vocal in opposing the concept of the Human Genome Project. Biology research in the public sector had always been done with support for single laboratories, often in great competition with each other, and there was concern from some that having a worldwide, multilab project like this would somehow ruin the culture and funding of biology research.

The perseverance and belief in the project by the proposers paid off when several groups, including Myers’, were awarded the first grants for the Human Genome Project in October 1990. A short time later the great value of the data from the project became obvious, even to most of the naysayers.

HudsonAlpha faculty investigators Jane Grimwood and Jeremy Schmutz were members of Myers’ team at the Stanford Human Genome Center and contributed greatly to the project. Grimwood, a senior scientist at the time, led a group that was responsible for finishing and performing quality analysis on the 320 million base pairs of human chromosomes 5, 16 and 19.

“I feel very lucky to have been a part of the Human Genome Project,” Grimwood said. “It was arguably the best international collaborative project of our lifetime, and became a catalyst for the genomics revolution that we have been, and will continue, experiencing.”

Schmutz joined the Sequencing Group at the Stanford Human Genome Center in 1996 to develop the computer programs for large-scale DNA sequencing, which helped the center with efforts to sequence chromosomes 5, 16 and 19. Schmutz was part of the group that finished and assembled the human sequence of these chromosomes, and led the quality assessment of the human genome sequence that evaluated the accuracy and completeness of the final human genome sequence.

The Human Genome Project consortium set a deadline of April 9, 2003, for submitting data for the finished sequence. Because the Stanford Human Genome Center was the westernmost lab participating in the project, Schmutz submitted data for the three chromosomes throughout the day and submitted the last data for the entire project by pushing the button for the last chromosome a mere 18 minutes before the midnight deadline.

“Our team worked endless hours to complete and finish our human chromosomes,” Schmutz said. “I built the final representation of the chromosomes from the underlying sequenced clones and submitted them to NCBI to go into the complete build. After the build, I sent an email to a friend in which I said, ‘It remains to be seen what real-world advances will come from the genome, but I’m hopeful for the future.’”

The real-world advances that stemmed from the knowledge and data resulting from the Human Genome Project are innumerable, having profound positive impacts on not only human health and disease but also diverse fields like renewable energy development, food and agriculture, and industrial biotechnology.

The legacy of the Human Genome Project

The vision of HudsonAlpha rests on the foundation established by the Human Genome Project. Hudson once said that the genomics-focused institute was started based upon the basic question of “Where are we going to take the sequence and the results of the Human Genome Project now?” HudsonAlpha was founded, and continues to operate today, on the goal of moving advancements in genomics to improve the human condition. The Human Genome Project means even more to HudsonAlpha because it was through the project that Hudson met Myers.


Basic biological discovery

  • Today, genomics permeates the world, from ancestry to forensics to human health to agriculture.
  • The Human Genome Project helped lay the groundwork for discovery-driven science, including important consortium projects like the Encyclopedia of DNA Elements (ENCODE) Project consortium and the Cancer Genome Atlas, both in which HudsonAlpha researchers participated.
  • At HudsonAlpha, genomics is at the core of discovery in human health and disease, agricultural and basic biological research.
  • HudsonAlpha researchers apply genomic technology to uncover the genetic causes of diseases including cancerneurological disorderschildhood diseases and autoimmune diseases.
  • Researchers at the HudsonAlpha Center for Plant Science and Sustainable Agriculture are applying the techniques of genomic research to plants and agriculture with the ultimate goal of accelerating discoveries in crops and developing new scientific methods that will change the way we grow and use plants in agriculture.

Technological advances

  • Since the completion of the Human Genome Project, whole genome sequencing technology has advanced and become more cost-effective. The technology can now be more readily applied in basic and clinical research settings.
  • HudsonAlpha researchers use whole genome sequencing as a routine part of many research studies.
  • As part of the Clinical Sequencing Exploratory Research (CSER) program, HudsonAlpha faculty researchers Myers, Dr. Greg Barsh, Greg Cooper, Neil Lamb, Shawn Levy and genetic counselor Kelly East are working with physicians, scientists and genetic counselors at partner institutions to sequence the genomes and exomes of hundreds of north Alabama children and their families.
  • HudsonAlpha is part of the SouthSeq project, which is a National Institutes of Health-funded research study looking at how whole genome sequencing can be used to try to find the reason for medical problems among newborns in a neonatal intensive care unit.

Culture of research

  • A major hallmark of the Human Genome Project was the rapid, free release of data. This was important to those involved in the project because it allowed others to start using the genome data immediately without having to wait 13 years for the final publication.
  • Grimwood and Schmutz are still firm supporters of rapid, free sharing of scientific discoveries. At the HudsonAlpha Genome Sequencing Center, of which the two are co-directors, they sequence and make publicly available de novo genomes, which leads to discovery in plant sciences.
  • The Human Genome Project paved the way for consortium-based research projects, several of which HudsonAlpha researchers have been involved in through the years.
  • The Myers Lab has been a member of the Encyclopedia of DNA Elements (ENCODE) Project consortium for nearly two decades. As a follow-up to the Human Genome Project, ENCODE is a worldwide effort to understand how the human genome functions.

(Courtesy of Alabama NewsCenter)

10 mins ago

This weekend’s college football TV schedule

For a printable version, click here. Pro tip: Save the image below to your phone for quick and easy access all weekend.

(Note: All times are Central)

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Zack Shaw is a contributing writer for Yellowhammer News and former walk-on for the Auburn Tigers. You can contact him by email: zack@yellowhammernews.com or on Twitter @z_m_shaw

Hayden Crigler is a contributing college football writer for Yellowhammer News. You can contact him through email: hayden@yellowhammernews.com or on Twitter @hayden_crigler.

1 hour ago

Bama gunning for greatest season ever; #NeverDabo trends again; Malzahn within reach of a milestone, maybe

Nick Saban’s absence from the sidelines of the Iron Bowl may only add to the legend of what is unfolding as the best season ever played by a college football team.

Similar banter occurred last year in the midst of LSU’s run to the national title. It seemed legitimate to at least consider it given the production on the offensive side of the ball. Yet, one cannot help but think much of the LSU discussion happened because the bar was set so low going into the 2019 season. The shock and surprise that Ed Orgeron and a previously average transfer quarterback could put it all together made the feat seem that much bigger.

There has been no element of surprise in Tuscaloosa, which makes for a more solid case.

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Saban, through various coordinators, has recently installed some of the most explosive offenses in the country year after year. And the old defensive wizard has fielded in 2020 a unit with elite athleticism and speed.

After six games last year, LSU’s offense was averaging 536 total yards per game. In the same amount of games this season, Alabama’s offense is racking up 555 yards per game.

Through six games, Mac Jones has a passing efficiency rating of 210.3. Joe Burrow’s rating was 204.5 at the same point last season. Burrow was leading the nation in completion percentage after six games, in what would end up being a Heisman Trophy-winning season, at 78.8%. Jones is completing 78.5% of his passes.

With an offense churning out those kind of historic numbers, not much is required of the other side of the ball.

Excluding its performance against Ole Miss, which has proven to be an aberration, the Tide is a top 25 defense with a ton of disruptive potential on the back end. This is a nearly identical spot at which LSU sat last year.

Alabama is 7-0 with everything, including history, out in front.

#NeverDabo

For a minute this week, all fanbases united against Dabo Swinney.

Dabo had the audacity to stand up for his team and his program after his Clemson Tigers hauled all the way to Tallahassee only to have their game against the hometown Seminoles canceled.

Florida State did not feel comfortable with Clemson’s health protocols. Dabo, in turn, expressed his disappointment with the entire situation.

No doubt Dabo has some problems on the field that would seem to be more pressing, including a secondary devoid of athleticism and an offensive line which is downright bad. Clemson’s roster pales in comparison to Alabama’s.

Still, Dabo committed a notable criminal act this week which brought him the flack.

His crime was that he spoke like a football coach.

Dabo did not get the memo that you may only speak about college football in 2020 if your remarks include an irrational fear of the virus.

He did what football coaches have done for as long as the ball has been snapped, he spoke to his team through the media.

After taking a tough loss against Notre Dame and spending two weeks preparing to get back on its feet, Dabo’s Tigers got the rug pulled out from under them less than two hours before kickoff. In seeking to get his players’ minds right and motivated for another week of practice, Dabo teed off on FSU’s decision to cancel the game and vigorously defended his program’s commitment to safety. Not to mention that in the days leading up to the initial college football rankings, he used the opportunity to create a diversion of focus.

Tide fans jumped in quickly to sit in reserved #NeverDabo seats.

Reminded of the fact that they have never liked Dabo, Auburn fans saw this week’s events as a way to kill two birds with one stone.

Then there was the national media who has never liked Dabo and still thinks the entire season should have been canceled.

Here is an idea, maybe it is possible to coach hard, motivate your players, stand up for your team and be diligent in how you operate your program.

None of those things are mutually exclusive.

Let’s get to a special Iron Bowl edition of all underdog picks.

BLACK FRIDAY

UCF (-25) at South Florida: Someone famous once said, “There’s an old saying…fool me once, shame on you. Fool me, can’t get fooled again.” Well, he would not like what is about to happen here. We have taken South Florida as a big underdog at home once before, and it did not end well for us or the Bulls. UCF is coming off an emotional fourth quarter loss to No. 7 Cincinnati. First-year head coach Jeff Scott is building a foundation in Tampa. It continues today. Can’t get fooled again.

The pick: UCF 40, South Florida 20

No. 2 Notre Dame (-5.5) at No. 19 North Carolina: Believe it or not, North Carolina has been a bit of a disappointment this season. It will be interesting to see just how many more years Mack Brown is willing to commit to his second trip through Chapel Hill. If the over/under is 2 more seasons, we will take the under. Going back to his time at UAB, Brown has always been a big game coach. Bryan Kelly and the Irish will be happy to get out alive.

The pick: Notre Dame 43, North Carolina 40

No. 13 Iowa State at No. 17 Texas (-1): Every once in a while college football fans are forced to stop and think about the fact that Tom Herman coaches at Texas and Matt Campbell is the head man at Iowa State. It should be the other way around. While Iowa State is incredibly well-coached, Texas probably has the superior 1-22. Probably.

The pick: Iowa State 27, Texas 23

No. 15. Oregon (-14) at Oregon State: Do enough people in the state of Oregon really care about college football to warrant calling this rivalry “The Civil War”? Doubtful. One of the more predictable aspects of this season is that Oregon misses Justin Herbert.

The pick: Oregon 26, Oregon State 24

THE BASICS

Pittsburgh at No. 3 Clemson (-25): Even Dabo cannot think Clemson is the third-best team in the country. Instead of complaining about Dabo’s FSU rant, maybe the warriors in the national sports media should be asking for a playoff committee competency hearing. The Panthers have oddly been a tough out for Clemson in Death Valley.

The pick: Clemson 30, Pittsburgh 20

No. 20 Coastal Carolina (-17) at Texas State: We have had our eye on this game for more than a few minutes. Coastal Carolina comes off of a big win against rival Appalachian State and now must make the cross country trek to San Marcos, which is not the easiest outpost to reach. Former Texas A&M offensive coordinator, and current Texas State head coach, Jake Spivatal is seeing his Bobcats struggle through a tragic week, though. Defensive back Khambrail Winters was fatally shot on Tuesday during a drug deal gone bad. Not an easy situation for Spivatal.

The pick: Coastal Carolina 33, Texas State 29

THE IRON BOWL

No. 22 Auburn at No. 1 Alabama (-24.5): An Auburn win would mean that head coach Gus Malzahn takes sole possession of the winningest record against Nick Saban during his time at Alabama. Or would he? Malzahn’s overall record lends to the belief that he is the best coach to ever walk the turf at Jordan-Hare. The air would get a lot thinner if Malzahn were to pick up his fourth victory over Saban. No one else has accomplished that. But does a win Saturday count against Saban? The Tide head coach’s COVID-induced absence on the sideline could call that into question. Malzahn and his teams have never been intimidated by Alabama. There is no reason to think any different this weekend.

The pick: Alabama 44, Auburn 32

Tim Howe is an owner of Yellowhammer Multimedia

19 hours ago

State Sen. Elliott: ‘I am not interested in discussing’ the I-10 Mobile Bay proposal until we have a new governor, ALDOT director

According to a report last week, efforts were underway for the Eastern Shore Metropolitan Planning Organization (MPO) to put a new I-10 Mobile Bay Bridge proposal back on its Transportation Improvement Program (TIP) after being removed in 2019 to prevent the Alabama Department of Transportation (ALDOT) from proceeding with a controversial toll bridge proposal.

Under ALDOT’s public-private partnership plan, backed by Gov. Kay Ivey, travelers across the bridge that would have connected Mobile and Baldwin Counties would have paid $6 each way.

State Sen. Chris Elliott (R-Daphne), whose district is adjacent to the proposed project’s site, expressed his shock the proposal was back on the table during an appearance on Mobile radio FM Talk 106.5’s “Midday Mobile.” He also signaled his distrust of Ivey and ALDOT Director John Cooper for the way they had proceeded in the past.

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“[I] was a little bit taken aback that was even being brought up again — not because the project is not needed, that is for sure,” he said, “not because we don’t need to figure out a way to move people and commerce back and forth and back and forth across the region a whole lot easier and more efficiently. But just because of the manner in which this was handled by the governor and her administration. But I just cannot believe it is even being seriously discussed again.”

Elliott argued the Eastern Shore MPO’s decision to take it out of the TIP was the “last line of defense” for residents and elected officials that opposed the project. He said given that the Ivey administration was willing to proceed despite residents’ wishes, he was not interested in discussing the project until there was a new governor and ALDOT director.

“[T]o be clear — what has happened, the news is this will be going back on the Eastern Shore MPO’s visionary list,” Elliott said. “That puts it back into the MPO’s plan for consideration once a planning source has been identified. And their caveat is the funding source has not yet been identified. Of course, that is where we got hung up last time. But I’m going to tell you — the bigger issue here is not the funding source. It is not the need of the bridge. It is that the MPO, the Eastern Shore MPO specifically, was the last line of defense to keep this from happening. As the former chairman of the MPO, I know that all too well. That was how it got stopped. This governor and this ALDOT director were more than happy to proceed with a funding scheme and mechanism that was completely unfair for residents of coastal Alabama, that was objected to by every elected official I know of. And yet, they were perfectly willing to proceed with it.”

“So, I would say the issue with this project is not necessarily the need for it or even the funding mechanism for it — although that is obviously a problem if it involves a toll,” he continued. “But rather — it is an issue of trust with this administration, with this ALDOT director. That, if you will forgive the pun, that bridge is burned. It has not been rebuilt, and I doubt that it will be.”

“I am not interested in discussing this bridge or a Bayway proposal at all until we have a new governor and a new ALDOT director,” Elliott added.

@Jeff_Poor is a graduate of Auburn University and the University of South Alabama, the editor of Breitbart TV, a columnist for Mobile’s Lagniappe Weekly, and host of Mobile’s “The Jeff Poor Show” from 9 a.m.-12 p.m. on FM Talk 106.5.

20 hours ago

NFIB Alabama: Small Business Saturday especially important this year

It’s especially important this year for people to shop small on Small Business Saturday, says National Federation of Independent Business (NFIB) Alabama State Director Rosemary Elebash.

A release outlined that Alabamians can do so in person, online or over the phone.

Small Business Saturday, as it is annually, is this coming Saturday, the one immediately following Thanksgiving. However, this year’s Small Business Saturday may be the most important one ever, as hardworking small business owners and employees continue to be hit hard by the COVID-19 pandemic.

“The coronavirus is taking a toll on Alabama’s small businesses,” Elebash stated. “Governor Ivey has gradually eased many of the restrictions put in place to keep customers and employees safe, but small business owners say it may be months, perhaps years, before the local economy fully recovers from the pandemic.”

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“Small business is the backbone of our economy, making up 99.4 percent of all employers in the state. And while it makes headlines whenever a big corporation adds a few hundred jobs here or there, small businesses are responsible for a net increase of 23,841 jobs statewide in 2019,” she continued.

Small Business Saturday 2020 comes as a coalition led by the Business Council of Alabama (BCA) — and including NFIB Alabama — continues to undertake the Keep Alabama Open campaign.

“Our small businesses were doing well at the beginning of the year,” Elebash added. “Since spring, however, many people have lost their jobs or had their hours greatly reduced, while employers have had to learn new safety procedures and invest in additional equipment from hand sanitizer stations and face masks to plastic shields at the checkout. Some small businesses intended to close temporarily and wound up closing for good.”

“That’s why we need to make a point of supporting local shops and restaurants, not just on Small Business Saturday but throughout the holiday shopping season,” she explained. “If you can’t visit them in person, then order online or place your order by phone and take advantage of local delivery or curbside pickup. Or, buy gift cards that you can redeem once the crisis is over.”

“Alabama’s economy is built on its small businesses,” Elebash concluded. “Without our support, we could lose them, and that would be bad for everyone.”

RELATED: Why Small Business Saturday really matters in 2020

Sean Ross is the editor of Yellowhammer News. You can follow him on Twitter @sean_yhn

21 hours ago

Alabama Power joins industry partners to raise awareness on scams

Alabama Power partnered with utilities across the nation through Utilities United Against Scams (UUAS) to recognize the fifth annual Utility Scam Awareness Day on Wednesday, Nov. 18. Utility Scam Awareness Day is part of International Scam Awareness Week, an advocacy and awareness campaign focused on educating customers and exposing tactics used by scammers.

“Alabama Power is joining with our partners on Utility Scam Awareness Day with one goal in mind – to protect our customers against scams,” said Alisa Summerville, Customer Service Center director for Alabama Power. “We’ve seen a higher number of scammers trying to take advantage of our customers during the coronavirus pandemic, and this is another opportunity to equip our customers with information to identify and combat scams.”

Alabama Power is sharing tips to help customers protect themselves from false tactics used by scammers. Customers should know that Alabama Power:

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  • Will never call to demand an immediate payment.
  • Will never call to request bank or credit card information.
  • Will never come to your door to demand an immediate payment.

Here are ways to spot scams from Alabama NewsCenter on Vimeo.

Customers with any questions about the status of their Alabama Power account should not hesitate to call Customer Service at 1-800-245-2244. The automated voice system is available 24 hours a day to check account balances and status. Customers can reach a Customer Service agent weekdays from 7 a.m. to 9 p.m. at 1-800-245-2244.

“A simple tip for our customers: If you are unsure if a call is a scam, hang up and contact our Customer Service team at 1-800-245-2244,” Summerville added.

UUAS, a consortium of more than 145 U.S. and Canadian electric, water and natural gas utilities and their respective trade associations, continues to build awareness of common scams and new scam tactics being used during the pandemic. Through its work and with the help of customer reporting, UUAS has succeeded in taking out of operation nearly 6,000 toll-free numbers used by scammers against utility customers.

“It is no surprise that scammers have been seeking to exploit the heightened anxiety of people coping with the pandemic,” said UUAS founder and Executive Committee Chairman Jared Lawrence. “I am proud to report that UUAS education efforts and utilities well-publicized customer testimonials have prevented a drastic increase in victims. However, the relentless attempts by these criminals make it clear that we must continue to actively work to protect our customers and to keep scammers from casting confusion on our pandemic recovery messages.”

The Federal Trade Commission website provides additional information about protecting personal information and other information regarding impostor scams.

Visit www.utilitiesunited.org for more information and tips on how customers can protect themselves from impostor utility scams. Follow along with UUAS on Twitter and Facebook.

(Courtesy of Alabama NewsCenter)