Lilly Grossman had been suffering from painful muscle twitches that would wake her up multiple times a night, preventing both her and her parents from sleeping soundly for the past 13 years, writes Ed Yong at Not Exactly Rocket Science. After participating in Sarah and Eric Topol's Idiopathic Diseases of Man, or IDIOM, study — as part of which Lilly and her parents had both their genomes and exomes sequenced — researchers found mutations in two of Lilly's genes. "The team suspects that ADCY5 accounts for Lilly's shaking, while DOCK3 influences her balance and muscle weakness. It seems that she was born with extraordinary bad luck—a double-whammy of fresh mutations in two separate genes that conspired to produce her unique constellation of problems," Yong writes.

This did, though, suggest a possible treatment, and while that treatment hasn't been a cure, the frequency and severity of Lilly's tremors have lessened, Yong notes. "Treatments aren't going to be instantaneous or 100 percent, but they're hope," Steve Grossman, Lilly's father, tells Yong. "We gained hope. And the more data we have, the better position we'll be in to figure this out."

In PLOS One, researchers report on a genetic analysis of a 33,000-year-old dog skull found in a cave in Siberia's Altai Mountains. A team from the US, Russia, Finland, and Spain performed targeted mitochondrial DNA sequencing on jaw bone and tooth samples from the skull, showing that these samples matched one another and clustered genetically with domestic dogs. The aged canine remnants shared fewer genetic similarities with modern-day wolves or with ancient wolves from the Pleistocene period whose remains were recovered from the same cave. "These results suggest a more ancient history of the dog outside of the Middle East or East Asia," authors of the study say, "previously suggested as centers of dog origin."

For more on the study, check out a related story in our sister publication GenomeWeb Daily News.

Complex traits are often a consequence of common variants falling across many genes, according to a PLOS Genetics study. Researchers from Australia and Korea assessed genotyping data for almost 7,200 individuals from Korea, using a combination of genome-wide estimation and partitioning analyses to look at how well sets of common SNPs explained 49 complex traits — from obesity and blood pressure to liver, lung, and kidney functions. For almost all of the traits tested, SNPs spread across the genome seemed to explain a considerable proportion of the trait's heritability, pointing to widespread polygenicity among complex human traits, study authors argued. "Despite examples where a few variants explain a substantial amount of variation," they say, "all these results are consistent with polygenicity being ubiquitous for most complex traits."

A team from Nigeria and Israel cataloged vector-borne pathogens found in Nigerian dogs and three tick species that pester them for a study in PLOS Neglected Tropical Diseases. The researchers used targeted PCR sequencing to track down vector-borne pathogens in blood and tick samples taken from 181 dogs in Nigeria. The analysis uncovered a wide range of pathogens known for infecting either animals or humans, they note, with around 63 percent of the ticks and more than three-quarters of the dogs apparently carrying at least one vector-borne pathogen.

In a guest post at the Genomes Unzipped blog, two researchers from the University of California, Berkeley, discuss how genotype imputation could help consumers get more information out of their 23andMe testing results by predicting or "imputing" variants that are not assayed by the genotyping chip.

Berkeley's Peter Cheng and Eliana Hechter say that the imputation process involves comparing 23andMe data — or data from some other direct-to-consumer testing company — with a reference panel from the 1000 Genomes or HapMap projects. Since these reference datasets have a much larger pool of SNPs than DTC chips test for and because humans have a common genetic ancestry, the imputation algorithms can predict other variations that would likely be present in the user's genome if it was fully sequenced.

Basically, "the imputation algorithm models your genome as a mosaic of related genomes, and uses these related genomes to fill in all of your missing data," the post says.

There are different programs that can be used to predict genotypes. Hechter and Cheng say they used one called Impute2 which was developed by a team from the University of Oxford. They've also written a handy script that transforms 23andMe raw data files into a format that is compatible with Impute2.

Hechter and Cheng do note that 23andMe updates its genotyping chip from time to time and customers can upgrade their data for a fee.

And the results appear to be quite accurate, according to the post. "To give a rough idea, the average confidence was 97.58 percent across all SNPs [Cheng] imputed in his own genome," they write.

Also, Hechter says she was able to impute BRCA2 variants that she quite likely has, which are not included on the 23andMe chip.

In this week's Science, a team led by researchers from Heinrich Heine University and Oklahoma State University report on the discovery that the red alga Galdieria sulphuraria, which lives in the toxic conditions of volcanic sulfur springs, acquired some of the genes it needs to survive from simpler organisms such as bacteria. The investigators sequenced the alga's genome and found acquired at least 75 genes through horizontal gene transfer. Around 5 percent of the alga's protein-coding genes were transferred from prokaryotes in this manner, including ones involved in "ecologically important processes ranging from heavy-metal detoxification to glycerol uptake and metabolism," the researchers write.

Also in Science, scientists from GlaxoSmithKline and Stanford University urge the inclusion of patients' clinical, social, and environmental histories along with genomic data to develop true personalized medicines. Focusing on genomics alone without giving consideration to other factors that affect patient outcomes could lead to "depersonalized" medicine, they warn, adding that an "emphasis on personal attributes of patients and their environments, and to incorporate these features into an enriched approach to personalized medicine" is needed to "complement the power of genomics."

The Cancer Genome Atlas is set to finish up next year after sequencing some 10,000 samples from about 20 different cancer types. TCGA has found, ScienceInsider notes, a number of new cancer genes and confirmed others that were previously identified. But with its price tag reaching over $375 million, some critics say it has been too expensive, though many disagree.

At a National Cancer Institute meeting earlier this week, Louis Staudt and Stephen Chanock discussed what could be a next step — by sequencing even more samples, say 10,000 per tumor type, researchers could uncover rare variants contributing to the disease, ScienceInsider adds. Further, it could enable studies examining the interplay of genetics and environmental factors.

However, with the agency facing a 5 percent budget cut, such a grand project might not be realized. ScienceInsider also notes that some skeptics said that the project might reach a level of "diminishing returns." According to ScienceInsider Cold Spring Harbor Laboratory's Bruce Stillman noted that he is a supporter of TCGA, but that taking it to such a new scale "is not very sensible at the moment."

In Nature this week, a team from Wageningen University reports on the identification of a gene that regulates the initiation of tuber development and plant maturity in potatoes. The plant originated in the Andes and evolved short day-dependent tuber formation as a propagation strategy. In more northern latitudes such as the US and Europe, potatoes needed to adapt to being grown in long-day conditions. The researchers identified a gene responsible for early tuberization in such an environment and suggest that the trait helped form the basis for the plant's domestication in northern countries.

Meanwhile, in Nature Genetics, researchers from the University of Michigan describe newly identified genetic variants associated with age-related macular degeneration. They conducted a meta-analysis of genome-wide association studies for the disease, including over 17,000 individuals with advanced AMD and 60,000 healthy controls. They found seven genomic regions newly associated with AMD risk and 19 associated regions overall, providing "new directions for biological, genetic and therapeutic studies of AMD."

Our sister publication GenomeWeb Daily News has more on this report here.