Massachusetts remains second in the number of grants awarded through federal stimulus funding for biomedical research, after a new batch of grants were announced today by the White House.

With 1,148 grants made through the American Recovery and Reinvestment Act of 2009 to date, the state trails only California's 1,604, in keeping with earlier grant totals tallied in this Sept. 4 Globe story.

Among the newly funded projects is a $4.5 million joint effort by scientists at Children's Hospital Boston, the Cambridge-based Broad Institute, and Harvard Medical School to sequence whole genomes of people with autism. Dr. Christopher Walsh of Children's, Michael Greenberg of Harvard, and Stacey Gabriel and Dr. David Altshuler of the Broad are the co-investigators.

Their work will build on Walsh's earlier studies of 85 Middle Eastern patients who share ancestors and recessive forms of autism. The researchers will sequence their DNA to pinpoint disease-causing genes and also study parts of their genome that don't code for proteins -- sometimes called "junk DNA" -- but might influence gene activity related to autism. Gene activity in brain cells will also be examined.

Part of the federal Grand Opportunity program to spur research activity, the grant must be spent within 18 months.

Massachusetts has made a strong showing in a $348 million federal grant program that encourages biomedical researchers to engage in high-risk projects with the potential to accelerate the translation of research discoveries into treatments.

Eleven of 42 Transformational R01 grants are flowing to scientists in the state and 12 of 55 New Innovator award winners are based here. One of 18 Pioneer Award recipients is from Massachusetts. All three programs from the National Institutes of Health are designed to spur exploration that may have been deemed too risky in past rounds.

A research collaboration based in Boston has won a five-year, $15 million grant to study how the hepatitis C virus defies immune system efforts to defeat it.

The Cooperative Center for Translational Research in Human Immunology, which will be based at Massachusetts General Hospital, won the grant from the National Institute of Allergy and Infectious Diseases, the hospital said. Dr. Raymond Chung, director of hepatology in the MGH Gastrointestinal Unit, will co-direct the new center with Dr. Paul Klenerman of Oxford University.

The center also includes researchers from MIT, Harvard, the Broad Institute of MIT and Harvard, Dana-Farber Cancer Institute, and the Wistar Institute, in Philadelphia.

Hepatitis C is a viral, blood-borne disease that can cause a life-threatening liver infection. Some people recover from the infection, but for most people the illness is chronic. The center will explore how the immune system fails to suppress and remove the virus.

Massachusetts ranks first in the number of early-career scientists to win prestigious grants in a national program designed to encourage innovation when research dollars are scarce.

Ten researchers -- from Harvard, Massachusetts General Hospital, MIT, and University of Massachusetts Medical School -- are among 50 scientists who have won six-year appointments to the Howard Hughes Medical Institute. California ranked second, with eight winners.

The $200 million Early Career Scientist program pays the salaries of the scientists and gives them each $1.5 million to fund their research.

The program was created last year to help scientists establish their own research programs amid a tighter funding climate that was harsh for people at the start of their independent careers. Candidates must have led their own laboratories for two to six years. A total of 2,000 applicants sought the appointments, which support the scientists at their home institutions.

A research group led by Boston scientists has found a gene whose defects cause a familial form of ALS, the devastating neurological disorder better known as Lou Gehrig's disease.

Ten percent of amyotrophic lateral sclerosis cases are inherited. The disease has been traced to only a few gene mutations that lead to the death of nerve cells that send messages to muscles. Most people develop ALS in middle age, becoming progressively weaker and then paralyzed, usually dying of respiratory failure within two to five years. About 30,000 Americans have the disease, according to the ALS Association.

A team from Massachusetts General Hospital, the Broad Institute, MIT, and other institutions write in tomorrow's Science about their discovery of a fourth gene whose 13 mutations caused ALS in a family of Cape Verdean origin. In another Science paper, a group in England reports two more mutations in the same gene that were found in eight British families.

"Every time a new gene like this is found, it illuminates a new pathway for triggering the disease," senior author Dr. Robert H. Brown Jr. said in an interview. "Once one has the gene, one can make a mouse model or cell model for this disease, which should accelerate efforts to find therapies for it."

A Boston cancer researcher has won one of three national prizes awarded to early-career scientists working on novel approaches to fighting cancer.

John L. Rinn, a researcher at Beth Israel Deaconess Medical Center and a faculty member of both the Broad Institute and Harvard Medical School, has received a three-year, $450,000 award from the Damon Runyon Cancer Research Foundation, the New York-based philanthropy announced today.

Rinn's research involves RNA molecules that may have a role in tumor formation and the spread of many types of cancer.

The other two awards went to Dr. Muneesh Tewari of Fred Hutchinson Cancer Research Center in Seattle, for work on early detection of ovarian and lung cancers, and to Dr. Ivan Maillard and Dr. Yi Zhang of the University of Michigan for improvements in bone marrow transplant safety.

A team led by researchers in Cambridge and Boston has more than doubled the number of genetic mutations implicated in the most common form of lung cancer.

The Tumor Sequencing Project decoded and sequenced 623 genes from 188 lung tumors in the largest genomic study to date of lung cancer, the leading cause of cancer deaths worldwide. Writing in tomorrow's advance online edition of Nature, scientists from the Broad Institute of Harvard and MIT, Dana-Farber Cancer Institute, and other institutions report finding 26 frequently altered genes in lung cancer.

Some of the newly discovered genes and the molecular processes they are involved in are also known to be flawed in other cancers, the researcher say. The findings and the genomic study used to reach them should be applied to other cancers, the authors say.

The work "gives us hope that targeted therapies could be used across multiple cancer types," co-senior author Matthew Meyerson of the Broad, Dana-Farber, and Harvard Medical School said in a statement.

The Broad Institute of Harvard and MIT is one of four centers chosen to map the epigenome, the collection of processes that control genetic activity in human cells.

The National Institutes of Health will invest more than $190 million over the next five years to better understand how epigenetic mechanisms affect health. The Broad's five-year, $15 million grant will support the study of at least 100 types of human cells, including human embryonic stem cells, adult stem cells, and others. The project will be led by Dr. Bradley E. Bernstein of the Broad and MIT and Alexander Meissner of the Broad and Harvard.

The other three Reference Epigenome Mapping Centers are at the Ludwig Institute for Cancer Research in San Diego, the University of Washington in Seattle, and the University of California, San Francisco.

Other parts of the NIH epigenomics initiative will concentrate on data analysis and coordination, technology development, and creating chemical tags to mark the epigenomes of mammalian cells.

Boston-area research institutions tied with California universities to each win a dozen federal grants designed to foster innovative research at a time of tight funding.

Twelve of 47 winners announced today by the National Institutes of Health are scientists working at Harvard, MIT, and Harvard-affiliated hospitals in Boston. California also had 12 winners from Stanford, the University of California, and Cal Tech. Last year 16 of 41 winners were from Greater Boston and seven were from California.

A sweeping survey of cancer genes has turned up previously unknown mutations that lead to brain cancer and possibly explain resistance to a common chemotherapy drug used to treat it, Boston researchers from a multi-center team report.

A paper appearing in Nature describes a systematic analysis of 206 glioblastoma multiforme tumors, the kind of cancer that Senator Edward M. Kennedy has. The gene search results come from the Cancer Genome Atlas Research Network, a $100 million pilot project funded by the National Institutes of Health to test this kind of large-scale systematic approach to cancer research.

The gene survey confirmed five mutations already identified in brain tumors and found three new ones. The researchers also tracked disruptions in cellular function that the mutations led to, including problems with cell division, cell growth, and repair of DNA damage.