Daily Archives: April 23, 2017

The following is a script of Breeding out Disease which aired on Oct. 26, 2014. Norah ODonnell is the correspondent. Tanya Simon, producer.

There are few fields of medicine that are having a bigger impact on how we treat disease than genetics. The science of genetics has gotten so sophisticated so quickly that it can be used to not only treat serious diseases but prevent thousands of them well before pregnancy even begins. Diseases that have stalked families for generations - like breast cancer - are being literally stopped in their tracks. Scientists can do that by creating and testing embryos in a lab, then implanting into a mothers womb only the ones which appear healthy. While the whole field is loaded with controversy, those who are worried about passing on defective and potentially dangerous genes see the opportunity to breed out disease.

Norah ODonnell: Did you ever envision that you would have the capability you have today?

Dr. Mark Hughes: No, but thats the fun of science. Its constantly surprising you.

[Dr. Mark Hughes: Wow. Look at that.]

Dr. Mark Hughes is one of the scientists leading the way in a rapidly growing field known as reproductive genetics. He pioneered a technique called preimplantation genetic diagnosis, or PGD, an embryo screening procedure that can identify deadly gene mutations - and alter a childs genetic destiny.

[Dr. Mark Hughes: This ones got a minus two.]

Dr. Mark Hughes: We all throw genetic dice when we have children. But when you know the dice are loaded and that theres a really reasonable chance that your baby will have an incurable, dreadful condition, youre looking for an alternative.

Dr. Hughes helped develop PGD two decades ago to screen embryos for one disease: cystic fibrosis. Today, because of advances in the mapping of the human genome, he says it can be used to root out virtually any disease caused by a single defective gene.

Norah ODonnell: Let me do a rapid fire yes or no. Can you use PGD for Tay-Sachs?

Dr. Mark Hughes: Yes.

Norah ODonnell: Muscular dystrophy?

Dr. Mark Hughes: Yes.

Norah ODonnell: Sickle-cell anemia?

Dr. Mark Hughes: Yes.

Norah ODonnell: Hemophilia?

Dr. Mark Hughes: Yes.

Norah ODonnell: Huntingtons disease?

Dr. Mark Hughes: Its one of the most common disorders we test for, yes.

Norah ODonnell: Alzheimers disease?

Dr. Mark Hughes: If its a mutation in a particular gene that causes early onset, we can test for it, yes.

Norah ODonnell: So you can test for Alzheimers.

Dr. Mark Hughes: This is a small subset of a particular kind of Alzheimers that attacks very early in life.

Norah ODonnell: Colon cancer?

Dr. Mark Hughes: If we know which of the colon cancer genes, yes.

Norah ODonnell: Breast cancer?

Dr. Mark Hughes: We do it regularly.

Dr. Hughes lab is one of a handful in the country that provides this genetic testing, which is why 3,000 couples turn to him each year. Among them, Matt and Melinda, who asked that we not use their last name. If they hadnt done the embryo screening procedure, their four-year-old son Mason and his baby sister, Marian, might very well have been born with a genetic mutation that increases the risk of breast, ovarian, prostate, and pancreatic cancer. It wasnt until Melinda herself was diagnosed with an aggressive form of breast cancer seven years ago that she found out she carried that gene mutation known as BRCA1.

Norah ODonnell: Did you know what BRCA1 was?

Melinda: Not a clue.

But as it turned out, it had haunted her family for generations. At age 29, facing chemotherapy and a double mastectomy, Melinda was afraid that if she had children one day, they would also be cursed with that potentially deadly mutation.

Norah ODonnell: What did doctors tell you about the risk of passing on this BRCA mutation?

Melinda: Fifty percent. So flip a coin.

Norah ODonnell: And I bet that weighed on you even heavier.

Melinda: Yes. Its a lifetime of having to worry about it. And I just didnt want my kids to have to do that.

The best way to ensure that was to do embryo screening for the BRCA1 gene mutation, which Dr. Hughes says is among the fastest-growing parts of his business.

Dr. Mark Hughes: This takes the risk. For example, in breast cancer, it takes the risk if you have this mutation from 50/50 of passing it to the next generation down to less than one percent.

Play Video

Kendra Lesta tells Norah ODonnell about losing her son Christopher to a rare disease and why she did PGD to prevent passing it on again. Watch N...

But the screening isnt easy. All couples, even fertile ones, must first go through in-vitro fertilization, the process in which a mans sperm is injected into a womans eggs under a microscope to create embryos. Then, five days later, a tiny tube just one twentieth the diameter of a human hair is used to extract from each embryo one single cell to be genetically tested for disease.

Norah ODonnell: Its just one cell?

Dr. Mark Hughes: Yes.

Norah ODonnell: You can tell that much from one cell?

Dr. Mark Hughes: You can tell an awful lot in one cell.

That cell is packed up at fertility clinics across the country and shipped overnight in ordinary looking boxes like these to screening labs. We followed the process at Dr. Hughes lab, called Genesis Genetics just outside Detroit, where a team of scientists took over.

Norah ODonnell: So what do you do with that one cell when it arrives here?

Dr. Mark Hughes: Well were busy. We have to break the cell open; they have to pull out this enormous encyclopedia of genetic information.

Hes talking about the cells DNA, our genetic code that scientists represent with four letters - A, C, T and G. For a gene to work properly, the letters have to be strung together in the right order. If theyre not, that could spell trouble. Its Dr. Hughes job to find the mutation - or typo - in a gene that could cause disease.

Dr. Mark Hughes: So you have to find that typo in effectively six billion letters.

Norah ODonnell: A typo in six billion letters?

Dr. Mark Hughes: Yeah.

Norah ODonnell: So how do you do that?

Dr. Mark Hughes: Technology is amazing.

Dr. Hughes used the technology to screen Matt and Melindas embryos in 2010 - ruling out the ones that carried the BRCA1 mutation, which would have given their children a reasonable chance of getting breast or other cancers.

Norah ODonnell: About how many of them tested positive for the BRCA1 gene?

Dr. Mark Hughes: About half and indeed, if you look at her embryos, here is an affected, an affected, an affected, an affected. Thats four. Its about half. It is just what youd expect.

Its just what youd expect in nature. But with the powerful intervention of science, embryos that carry a harmful mutation are often discarded, which is one reason the decision to go ahead with the screening was a difficult one for Matt and Melinda.

Melinda: We prayed a lot about it. Its a hard decision to make.

Norah ODonnell: What did you struggle with?

Melinda: Was it right? Was it the right thing to do? Is it playing God? Is it ethical? And the more we learned about it and got comfortable with the idea, it was like, Yes, absolutely.

Norah ODonnell: You have said, The breast cancer stops with me.

Melinda: Yes. Its not just my children. Its their children and my grandchildren and great grandchildren. Forever and all for time, in my bloodline, yeah.

The entire process cost them around $16,000 - a small price to pay, Melinda says, for her childrens health.

But Anne Morriss didnt get to change the odds for her child. By the time she learned she carried a dangerous mutation, she had already passed it on to her son, whos now seven. At birth, Alec seemed the picture of health, but then came an unexpected call from a doctor.

Anne Morriss: He started by saying, Can you please go check and make sure that your child is still alive and then come back and we can continue this discussion.

Norah ODonnell: So a doctor calls you and says, I need to tell you something but can you go check that your son is still alive.

Anne Morriss: Thats how the conversation started.

Norah ODonnell: What was your reaction?

Anne Morriss: You know, your heart just falls out of you.

A newborn screening test revealed Alec had a rare and sometimes fatal metabolic disorder called MCAD deficiency; he had to be fed every few hours just to stay alive.

Unlike breast cancer, MCAD deficiency is a recessive disorder, meaning a child must inherit a copy of the faulty gene from both parents. Anne Morriss had used an anonymous sperm donor to conceive, but in an incredible case of bad luck, he just happened to carry the same mutation she did.

Anne Morriss: Every human being walking the planet is a carrier for a rare disease. But what matters is who we choose to partner with reproductively. Like, thats where the risk shows up.

Now she wants to reduce the risk of a bad genetic match for others - well before they start the reproductive process. She just started a company called GenePeeks with Lee Silver, a Princeton University professor whos also a molecular biologist -- though his latest idea doesnt take place in a lab. Its entirely virtual.

Lee Silver: We are creating digital babies.

Norah ODonnell: Digital babies?

Lee Silver: Yes.

Norah ODonnell: So youre simulating the process of reproduction, but on a computer.

Lee Silver: Exactly.

Silver says all it takes is a saliva sample to obtain DNA. He then combines the genetic information from both prospective parents in a computer to make a thousand digital babies.

Norah ODonnell: this is a digital baby.

Lee Silver: This is a digital baby.

It contains virtual DNA - which like real DNA, is represented by those same four letters - A, C, T and G.

Lee Silver: This baby has a mutation.

He says that by analyzing the DNA in all those digital babies, he is able to calculate the risk of two people conceiving a child with any one of 500 severe recessive pediatric disorders.

Play Video

On assignment for 60 Minutes, CBS News correspondent Norah O'Donnell describes how she created her own "digital babies"

For now, GenePeeks is available for $2,000 to clients using sperm banks and egg donors to conceive, though its founders say the goal is to expand it to all couples who want to have a baby.

Norah ODonnell: You think everyone whos going to have a baby should go and have a digital baby first?

Lee Silver: I see a future in which people will not use sex to reproduce. Thats a very dangerous thing to do.

That may sound far-fetched, but the way Lee Silver sees it, there will come a time when couples will no longer want to conceive naturally because its too risky.

Lee Silver: Its safer to have a baby with this pre-knowledge, this genetic information that might help them avoid disease.

But with the promise of this technology also comes the fear that some parents would want to use it to select genetic traits in their children that have nothing to do with disease - a debate Lee Silver himself stoked when he wrote the patent for GenePeeks.

Norah ODonnell: We read your patent and it says your technology could be used to assess whether a child could have other traits, like eye color, hair color, social intelligence, even whether a child will have a widows peak? If your company is so focused on preventing disease, why would you include those traits?

Lee Silver: The purpose of the list of traits is simply to demonstrate that our technology can be used to study anything thats genetically influenced. That doesnt mean were going to actually do that.

Norah ODonnell: OK. But youre running a company? That could be big business?

Lee Silver: We are the ones who invented this technology and were going to use it to study pediatric disease. At the moment, we will make sure the technology is used only for that purpose.

And at the moment, youll have to take his word for it because there are no real rules in this country limiting what this kind of technology can be used to screen for, leaving those decisions up to scientists like Lee Silver and Mark Hughes.

Norah ODonnell: So we should trust you to set the boundaries?

Dr. Mark Hughes: If Im setting a boundary saying, Im not willing to do that, thats no different from any other field of medicine. So sure.

Norah ODonnell: But do you wrestle with this at all? I mean, who is the gatekeeper?

Original post:
Breeding out disease - CBS News

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SALT LAKE CITY -- Saturday, Earth Day, marked the first ever March For Science, and people from around the world gathered in more than 600 cities.

The march evolved from a social media campaign to thousands of scientists and science enthusiasts taking to the streets.

In Utah, thousands marched in Salt Lake City, Logan, Moab, Park City, and Saint George.

I stand for science," said Heidi Redd, a San Juan County Rancher and Conservationist. "I will fight for science, and I must say that without science we would not be the leaders we are today.

Redd, a cattle rancher, said research done on grasslands and water conservation has helped her and others become leaders in agriculture.

For others, the importance of science goes far beyond the physical world.

As a person of faith, I think one of the greatest blessings God has given us is science, said Professor Brigham Daniels.

Daniels teaches environmental law at Brigham Young University and is the Chair of the Board of Directors for the LDS Earth Stewardship.

Daniels said he marched in support of his faith and his fight to protect the environment. Utah recently made its debut on a list of cities with the worst air pollution.

We owe it, not only to our kids, but we owe it to the elderly," Daniels said. "We owe it to the asthmatics. We owe it to ourselves.

Scientists and supporters at the march said it's a lot about taking care of our world and those in it, but it's also about making a political statement.

Professor Mario Capecchi teaches human genetics at the University of Utah. He's also a Nobel Laureate. He said more scientists should get involved in politics.

I take part of the blame," he said. "I think scientists, you know, were comfortable in the lab, but were not trained, we arent capable of communicating with the public, but we have to because we see terrible things are happening.

He went on to say change should have "happened yesterday", but he said now is better than never.

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Thousands of Utahns join worldwide March For Science - fox13now.com

April 21, 2017 by Sam Sholtis Penn State researchers identified 832 genes that have low coverage across multiple whole-exome sequencing platforms. These genes are associated with leukemia, psoriasis, heart failure and other diseases, and may be missed by researchers using whole-exome sequencing to study these diseases. Credit: Penn State University, Carley LaVelle

Whole-exome DNA sequencinga technology that saves time and money by sequencing only protein-coding regions and not the entire genomemay routinely miss detecting some genetic variations associated with disease, according to Penn State researchers who have developed new ways to identify such omissions.

Whole-exome sequencing has been used in many studies to identify genes associated with disease, and by clinical labs to diagnose patients with genetic disorders. However, the new research shows that these studies may routinely miss mutations in a subset of disease-causing genesassociated with leukemia, psoriasis, heart failure and othersthat occur in regions of the genome that are read less often by the cost-saving technology. A paper describing the research appeared online April 13 in the journal Scientific Reports.

"Although it was known that coveragethe average number of times a given piece of DNA is read during sequencingcould be uneven in whole-exome sequencing, our new methods are the first to really quantify this," said Santhosh Girirajan, assistant professor of biochemistry and molecular biology and of anthropology at Penn State and an author of the paper. "Adequate coverageoften as many as 70 or more reads for each piece of DNAincreases our confidence that the sequence is accurate, and without it, it is nearly impossible to make confident predictions about the relationship between a mutation in a gene and a disease. In our study, we found 832 genes that have systematically low coverage across three different sequencing platforms, meaning that these genes would be missed in disease studies."

The researchers developed two different methods to identify low-coverage regions in whole-exome sequence data. The first method identifies regions with inconsistent coverage compared to other regions in the genome from multiple samples. The second method calculates the number of low-coverage regions among different samples in the same study. They have packaged both methods into an open-source software for other researchers to use.

"Even when the average coverage in a whole-exome sequencing study was high, some regions appeared to have systematically low-coverage," said Qingyu Wang, a graduate student at Penn State at the time of the research and the first author of the paper.

Low-coverage regions may result from limited precision in whole-exome sequencing technologies due to certain genomic features. Highly-repetitive stretches of DNAregions of the genome where the same simple sequence of As, Ts, Cs and Gs can be repeated many timescan prevent the sequencer from reading the DNA properly. Indeed, the study showed that at least 60 percent of low-coverage genes occur near DNA repeats. As an example, the gene MAST4 contains a repeated sequence element that leads to a three-fold reduction in coverage compared to non-repeating sequences. Even when other genes have sufficient coverage, this region of the MAST4 gene falls well below the recommended coverage to detect genetic variations in these studies.

"One solution to this problem is for researchers to use whole-genome sequencing, which examines all base pairs of DNA instead of just the regions that contain genes," said Girirajan. "Our study found that whole-genome data had significantly fewer low-coverage genes than whole-exome data, and its coverage is more uniformly distributed across all parts of the genome. However, the costs of whole-exome sequencing are still significantly lower than whole-genome sequencing. Until the costs of whole-genome sequencing is no longer a barrier, human genetics researchers should be aware of these limitations in whole-exome sequencing technologies."

Explore further: Whole genome or exome sequencing: An individual insight

More information: Qingyu Wang et al. Novel metrics to measure coverage in whole exome sequencing datasets reveal local and global non-uniformity, Scientific Reports (2017). DOI: 10.1038/s41598-017-01005-x

Focusing on parts rather than the whole, when it comes to genome sequencing, might be extremely useful, finds research in BioMed Central's open access journal Genome Medicine. The research compares several sequencing technologies ...

(Medical Xpress)An international team of researchers has developed a way to use RNA sequencing to help in diagnosing patients with rare genetic muscle conditions. In their paper published in the journal Science Translational ...

Researchers have analysed 44 exome datasets from four different testing kits and shown that they missed a high proportion of clinically relevant regions. At least one gene in each exome method was missing more than 40 percent ...

UCLA researchers have found that a state-of-the-art molecular genetic test greatly improves the speed and accuracy with which they can diagnose neurogenetic disorders in children and adults. The discovery could lead directly ...

Published in today's edition of Nature, the research led by Dr Monkol Lek of the University of Sydney and Dr Daniel MacArthur of The Broad Institute of MIT and Harvard Universities reveals patterns of genetic variation worldwide ...

A new study that assesses the accuracy of modern human-genome-sequencing technologies found that some medically significant portions of an individual's DNA blueprint are situated in complex, hard-to-analyze regions that are ...

Whole-exome DNA sequencinga technology that saves time and money by sequencing only protein-coding regions and not the entire genomemay routinely miss detecting some genetic variations associated with disease, according ...

Research published this week in Scientific Reports uses computer image and statistical shape analysis to shed light on which parts of the face are most likely to be inherited.

Salk scientists and collaborators have shed light on a long-standing question about what leads to variation in stem cells by comparing induced pluripotent stem cells (iPSCs) derived from identical twins. Even iPSCs made from ...

In a study published today in PLoS ONE, a team of researchers reports solving a medical mystery in a day's work. In record-time detective work, the scientists narrowed down the genetic cause of intellectual disability in ...

After nearly 40 years of searching, Johns Hopkins researchers report they have identified a part of the human genome that appears to block an RNA responsible for keeping only a single X chromosome active when new female embryos ...

It's not so hard anymore to find genetic variations in patients, said Brown University genomics expert William Fairbrother, but it remains difficult to understand whether and how those mutations undermine health.

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Disease-associated genes routinely missed in some genetic studies - Medical Xpress