Exome sequencing shows potential as diagnostic tool

Blood samples

Credit: Graham Colm

In a large study, whole-exome sequencing provided 25% of patients with a diagnosis related to a known genetic disease, giving young

patients and their parents some long-sought answers.

The technology was able to detect a number of rare genetic events and new mutations contributing to disease.

Among the medically actionable findings were mutations related to Fanconi anemia, erythrocytosis, hemolytic anemia, and von Willebrand disease.

“The findings in this report, I believe, will forever change the future practice of pediatrics and medicine as a whole,” said study author James R. Lupski, MD, PhD, of the Baylor College of Medicine in Houston.

“It is just a matter of time before genomics moves up on the physician’s list of things to do and is ordered before formulating a differential diagnosis. It will be the new ‘family history’ that, better yet, gets you both the important variants inherited from each parent and the new mutations that contribute to disease susceptibility.”

This research was published in JAMA and is set to be presented on October 21 at the American Society of Human Genetics Annual Meeting in San Diego.

The researchers had previously conducted a pilot study of whole-exome sequencing that included 250 patients and revealed a 25% molecular diagnostic rate.

This current study included 2000 patients (88% pediatric) with clinical whole-exome sequencing analyzed between June 2012 and August 2014. The majority of patients—87.8%—had neurological disorders or a developmental delay, and 12.2% had non-neurological disorders.

The researchers collected peripheral blood, tissue, or extracted DNA samples from patients and their parents. The team sequenced patients’ DNA and compared those results to the normal reference. Any disease-associated mutations were then compared with the parent’s DNA to determine if the child inherited it from one or both parents.

In all, 504 patients (25.2%) received a molecular diagnosis, and 58% of the diagnostic mutations had not previously been reported. Two hundred and eighty patients had a single mutation that caused disease, 181 were autosomal recessive, 65 were X-linked, and 1 was presumed inherited through the mitochondria.

In 5 cases, the patient inherited 2 copies of the mutated gene from the same parent. Of the dominant mutations, 208 were de novo mutations not inherited from either parent, 32 were inherited, and 40 were not determined because parental samples were not available.

Among the de novo mutations, 5 demonstrated mosaicism, which suggested the mutation occurred after fertilization.

The researchers found 708 presumptive causative variant alleles in the 504 cases. Almost 30% of the diagnoses occurred in disease genes only identified by researchers in the last 3 years. In 65 cases, there was no available genetic test other than whole-exome sequencing to find the mutated gene at the time the test was ordered.

Twenty-three patients (about 5%) had mutations in 2 different genes, which could account for various aspects of the patient’s medical condition.

“Doctors generally try to find one diagnosis that explains all the issues a patient may have,” said study author Christine Eng, MD, of the Baylor College of Medicine.

“We have found that, in some cases, a patient may have a blended phenotype of 2 different conditions. That patients may have 2 different rare genetic diseases to explain their condition was an unexpected finding prior to the use of whole-exome sequencing.”

In the 2000 cases, incidental findings of medically actionable results that could result in early diagnosis, screening, or treatment were found in 92 patients. Three patients had more than 1 finding.

“Clinical exome sequencing can assist diagnosis in a wide range of disorders that are diagnostic dilemmas,” Dr Lupski said. “Rare variants and Mendelian disease are important contributors to disease populations. This is in sharp contrast to the thinking of population geneticists, who investigate how common variants contribute to disease susceptibility.”

“We find ‘rare variants’ in aggregate actually contribute to disease susceptibility in a big way. The individual diseases may be rare, but there are thousands of such diseases and many more being defined through genomics.”

Blood samples

Credit: Graham Colm

In a large study, whole-exome sequencing provided 25% of patients with a diagnosis related to a known genetic disease, giving young

patients and their parents some long-sought answers.

The technology was able to detect a number of rare genetic events and new mutations contributing to disease.

Among the medically actionable findings were mutations related to Fanconi anemia, erythrocytosis, hemolytic anemia, and von Willebrand disease.

“The findings in this report, I believe, will forever change the future practice of pediatrics and medicine as a whole,” said study author James R. Lupski, MD, PhD, of the Baylor College of Medicine in Houston.

“It is just a matter of time before genomics moves up on the physician’s list of things to do and is ordered before formulating a differential diagnosis. It will be the new ‘family history’ that, better yet, gets you both the important variants inherited from each parent and the new mutations that contribute to disease susceptibility.”

This research was published in JAMA and is set to be presented on October 21 at the American Society of Human Genetics Annual Meeting in San Diego.

The researchers had previously conducted a pilot study of whole-exome sequencing that included 250 patients and revealed a 25% molecular diagnostic rate.

This current study included 2000 patients (88% pediatric) with clinical whole-exome sequencing analyzed between June 2012 and August 2014. The majority of patients—87.8%—had neurological disorders or a developmental delay, and 12.2% had non-neurological disorders.

The researchers collected peripheral blood, tissue, or extracted DNA samples from patients and their parents. The team sequenced patients’ DNA and compared those results to the normal reference. Any disease-associated mutations were then compared with the parent’s DNA to determine if the child inherited it from one or both parents.

In all, 504 patients (25.2%) received a molecular diagnosis, and 58% of the diagnostic mutations had not previously been reported. Two hundred and eighty patients had a single mutation that caused disease, 181 were autosomal recessive, 65 were X-linked, and 1 was presumed inherited through the mitochondria.

In 5 cases, the patient inherited 2 copies of the mutated gene from the same parent. Of the dominant mutations, 208 were de novo mutations not inherited from either parent, 32 were inherited, and 40 were not determined because parental samples were not available.

Among the de novo mutations, 5 demonstrated mosaicism, which suggested the mutation occurred after fertilization.

The researchers found 708 presumptive causative variant alleles in the 504 cases. Almost 30% of the diagnoses occurred in disease genes only identified by researchers in the last 3 years. In 65 cases, there was no available genetic test other than whole-exome sequencing to find the mutated gene at the time the test was ordered.

Twenty-three patients (about 5%) had mutations in 2 different genes, which could account for various aspects of the patient’s medical condition.

“Doctors generally try to find one diagnosis that explains all the issues a patient may have,” said study author Christine Eng, MD, of the Baylor College of Medicine.

“We have found that, in some cases, a patient may have a blended phenotype of 2 different conditions. That patients may have 2 different rare genetic diseases to explain their condition was an unexpected finding prior to the use of whole-exome sequencing.”

In the 2000 cases, incidental findings of medically actionable results that could result in early diagnosis, screening, or treatment were found in 92 patients. Three patients had more than 1 finding.

“Clinical exome sequencing can assist diagnosis in a wide range of disorders that are diagnostic dilemmas,” Dr Lupski said. “Rare variants and Mendelian disease are important contributors to disease populations. This is in sharp contrast to the thinking of population geneticists, who investigate how common variants contribute to disease susceptibility.”

“We find ‘rare variants’ in aggregate actually contribute to disease susceptibility in a big way. The individual diseases may be rare, but there are thousands of such diseases and many more being defined through genomics.”

Blood samples

Credit: Graham Colm

In a large study, whole-exome sequencing provided 25% of patients with a diagnosis related to a known genetic disease, giving young

patients and their parents some long-sought answers.

The technology was able to detect a number of rare genetic events and new mutations contributing to disease.

Among the medically actionable findings were mutations related to Fanconi anemia, erythrocytosis, hemolytic anemia, and von Willebrand disease.

“The findings in this report, I believe, will forever change the future practice of pediatrics and medicine as a whole,” said study author James R. Lupski, MD, PhD, of the Baylor College of Medicine in Houston.

“It is just a matter of time before genomics moves up on the physician’s list of things to do and is ordered before formulating a differential diagnosis. It will be the new ‘family history’ that, better yet, gets you both the important variants inherited from each parent and the new mutations that contribute to disease susceptibility.”

This research was published in JAMA and is set to be presented on October 21 at the American Society of Human Genetics Annual Meeting in San Diego.

The researchers had previously conducted a pilot study of whole-exome sequencing that included 250 patients and revealed a 25% molecular diagnostic rate.

This current study included 2000 patients (88% pediatric) with clinical whole-exome sequencing analyzed between June 2012 and August 2014. The majority of patients—87.8%—had neurological disorders or a developmental delay, and 12.2% had non-neurological disorders.

The researchers collected peripheral blood, tissue, or extracted DNA samples from patients and their parents. The team sequenced patients’ DNA and compared those results to the normal reference. Any disease-associated mutations were then compared with the parent’s DNA to determine if the child inherited it from one or both parents.

In all, 504 patients (25.2%) received a molecular diagnosis, and 58% of the diagnostic mutations had not previously been reported. Two hundred and eighty patients had a single mutation that caused disease, 181 were autosomal recessive, 65 were X-linked, and 1 was presumed inherited through the mitochondria.

In 5 cases, the patient inherited 2 copies of the mutated gene from the same parent. Of the dominant mutations, 208 were de novo mutations not inherited from either parent, 32 were inherited, and 40 were not determined because parental samples were not available.

Among the de novo mutations, 5 demonstrated mosaicism, which suggested the mutation occurred after fertilization.

The researchers found 708 presumptive causative variant alleles in the 504 cases. Almost 30% of the diagnoses occurred in disease genes only identified by researchers in the last 3 years. In 65 cases, there was no available genetic test other than whole-exome sequencing to find the mutated gene at the time the test was ordered.

Twenty-three patients (about 5%) had mutations in 2 different genes, which could account for various aspects of the patient’s medical condition.

“Doctors generally try to find one diagnosis that explains all the issues a patient may have,” said study author Christine Eng, MD, of the Baylor College of Medicine.

“We have found that, in some cases, a patient may have a blended phenotype of 2 different conditions. That patients may have 2 different rare genetic diseases to explain their condition was an unexpected finding prior to the use of whole-exome sequencing.”

In the 2000 cases, incidental findings of medically actionable results that could result in early diagnosis, screening, or treatment were found in 92 patients. Three patients had more than 1 finding.

“Clinical exome sequencing can assist diagnosis in a wide range of disorders that are diagnostic dilemmas,” Dr Lupski said. “Rare variants and Mendelian disease are important contributors to disease populations. This is in sharp contrast to the thinking of population geneticists, who investigate how common variants contribute to disease susceptibility.”

“We find ‘rare variants’ in aggregate actually contribute to disease susceptibility in a big way. The individual diseases may be rare, but there are thousands of such diseases and many more being defined through genomics.”