Honorable Mention Excerpts

 

 

 

Emily Zhen

Naperville Central High School

Teaher: Nicholas DiGiovanni

 

Cancer genome sequencing offers a high-resolution, technologically advanced method for determining mutation frequency. While DNA sequencing glioblastoma, the most common and lethal brain tumor in adults, TCGA [Cancer Genome Atlas] researchers found that genetic alterations recurred in the phosphoinositide 3-kinase (PI3K) pathway, especially in the PIK3R1 gene (Ding et al., 2008). . .

 

. . . Inspired by the first sequencing of the human genome, researchers are collaborating to tackle one of the world’s most ancient and mysterious diseases. Even as the TCGA project draws to a close, scientists are undertaking new ventures involving DNA sequencing in the quest for a cure to cancer. Resulting in fruitful research endeavors, DNA sequencing has allowed scientists to decipher diseases like cancer one step, one nucleotide, at a time.

 

 

Sumit Dalsania

Eleanor Roosevelt High School

Teacher: Alexis Donoghue
 

DNA sequencing, or deciphering the order of nucleotide bases of DNA, has its beginnings in 1977 with the Sanger method of chain-termination sequencing. Employing 2’,3’-dideoxy and arabinonucleoside analogues of normal deoxynucleoside triphosphates to create chain-terminating inhibitors (Sanger, Nicklen & Coulsen, 1977), the procedure was a breakthrough in understanding the genetic sequence. However, it was also very tedious, requiring considerable time and relatively expensive reagents.

 

. . . The introduction of next-generation sequencing technologies has led to more economical sequencing costs along with an exponential increase of their use in various applications. . . From 2001 to 2012, the price to sequence an entire genome fell from over $95,000,000 to less than $7,000 (Wetterstrand, 2013). This ten-thousand fold decrease has out-paced Moore’s law of computing, serving as proof of the increasing financial feasibility of sequencing.

 

 

Claire Chen

Menlo School

Teacher: Todd Hardie

 

Maps unlock the potential to discover desired destinations, and perhaps even treasures. In 2003, the Human Genome Project (HGP) successfully mapped the 20,000-25,000 genes that make up the human genome by sequencing the approximately three billion constituent base pairs. It was expected that coveted treasures, such as cures for diseases like cancer, lay within A’s, G’s, C’s, and T’s of the human genome.

 

 . . .In 2002, the mutated B-RAF gene was found to be a human oncogene. Using a new DNA screening technique called capillary-based conformation-sensitive electrophoresis followed by the direct sequencing of polymerase chain reaction products, B-RAF gene mutations were found to be present in over two-thirds of the melanoma DNA samples. Researchers rapidly and efficiently compared the nucleotide sequences of cancer DNA to those of healthy DNA, allowing them to locate the mutated gene.

 


Brian Lue

The John Cooper School

Teacher: Holly Barlaam
 

Transposable elements (TEs) are “DNA sequence[s], copies of which become inserted into various sites in the genome” (Futuyma, 2009). Alu elements are a class of TEs in DNA that are found in all primates, including humans. The Human Genome Project revealed that 55% of our DNA consists of repetitive sequences, and Alu elements are the most abundant, making up about 10% of our DNA (Häsler & Strub, 2006). Although it has been shown that other mammals lacking Alu elements are perfectly healthy, the unusual abundance of them in humans suggests that they play a more significant role than just being junk DNA (Pray, 2008).

 

One interesting aspect of Alu elements involves [their] role in creating new exons through a process called exonization. This can add new abilities to existing genes or even create new genes (Pray, 2008). Research by Sela et al. (2007) showed that exonization occurred first when TEs were copied and spliced into introns. Throughout many generations, mutations activated these TEs and thus they became part of the exons.

 


Chloe Deshuesses

Carrboro High School

Teacher: Robin Bulleri
 

Data from the Human Genome Project changed the way that humans and researchers viewed DNA. Protein-coding genes in the human genome were estimated to be around 90,000 genes before the completion of the HGP, but are known to be closer to 20,000 today. The low number of genes has now been attributed to a cellular process called alternate splicing, where a gene can code for more than one protein depending on which sequences are considered exons during post-transcriptional processing (Zimmer, 2008). The variations of the RNA sequence may change the amino acids in the final protein and lead to changes in the structural fold or regulation of sequence sites. Additionally, 95% of human genes consisting of several exons in a transcript are spliced multiple ways and the final roles of the transcript vary depending on the type cell and tissue it is found in. The various possibilities for differentiation in the post-transcriptional stages contribute to biological complexity (Barash et al., 2012).

 

 

Trinish Chatterjee

Richard Montgomery High School
Teacher: Jerry Turner

 

Celebrating its decennial this year, the completion of the sequencing of the Human Genome and the knowledge, science, and technology that has arisen from it make it undoubtedly one of the greatest achievements in science of this era. The impact from the HGP can be grouped into two overarching categories: its direct impact to medicine and genomics and its indirect impact on biotechnology, both of which lead the HGP being a base for research to come.

 

…After the conclusion of the HGP, the demand for less costly and more efficient sequencing grew even more, and to answer that call again numerous companies started “next generation sequencing”. These methods included Pyrosequencing, Sequencing by Synthesis, and Sequencing by Ligation, among others, as more efficient, reliable, and cost-effective ways of processing DNA. This flurry of technology is owed to the huge contribution of the HGP for setting the stage for these technologies. This can be seen today in the huge drop in costs to sequence DNA per megabase, from >$1000 in 2001 to <$.10 in 2013, a 10,000 fold drop (5).

 

 

Jingwen Zhang
Thomas Worthington High School

Teacher: Jodi Bacon

 

…With the improvement of rapid genome sequencing, companies such as 23andMe have brought genetic innovations to the general populace, searching the genes of hundreds of thousands of people for certain targeted SNPs that increase or decrease risk for certain diseases and show carrier status. Non-invasive whole genome sequencing for fetuses, a way to use maternal plasma to explore the genetic information of one still in the womb, has recently been developed (Kitzman et al., 2012).

 

With the new knowledge the Human Genome Project introduced comes great responsibility, ushering in new and complex issues that scientists and society have to deal with. Despite the growth in genetic knowledge, the capacity and conclusiveness of genetics is easily overstated; beyond the impact of lifestyle and other environmental factors, the expression of genes coding for certain traits and characteristics still varies from person to person. A recent study found that one suffering from a genetically linked disease could have the same disease-causing variants in his genome as another healthy, fit individual (Xue et al., 2012).

 

 

David Qin

Lake Oswego High School

Teacher: Richard Rosenbaum

 

By sequencing our very own genome, we have found the means to look at ourselves from a genetic and molecular point of view, with vast consequences for our health, medicine, and our daily lives.

 

The Human Genome Project (HGP) had a profound impact on medical research. Having a genomic database to consult eliminated one of the major hurdles to research on Mendelian diseases.

 

…The HGP has also made possible the field of personal genomics. Using microarray-based single nucleotide polymorphism (SNP) genotyping, companies can inform patients about their ancestry, whether they are carriers or not, their risks for diseases, and whether they will suffer from reactions to drugs (Kung, J.T. and Gelbart M. E., 2012).

 

 

Evangeline Chandran
River Hill High School

Teacher: Terri Bradford
 

Since the sequencing of the human genome, genomics have contributed to the better understanding of human biology and improving human health [3, 4, 8]. As a result, new therapies have been developed by discovering new insights about cancer, the molecular basis for inherited diseases, and the role of structural variations in diseases.

 

…for example, genomic studies reveal regions of genetic variations resulting in the risk for Crohn’s disease. Genomic research to identify genetic variations in Crohn’s disease patients has enabled molecular, cell biological, and animal model studies that have led to a better understanding of Crohn’s disease and the development of novel therapies [4].

 

 

Jonathan Yu
Bergen County Academies
Teacher: Judith Pinto

 

The first animal to have its genome completely sequenced was the Caenorhabditis elegans. This transparent nematode is a roundworm only about 1 millimeter in length but contains a genome made up of approximately 20,000 genes. Only recently was it discovered that the human genome also contains approximately 20,000 genes. But how could this be possible?

…The human genome can be compared to a word document that is “read-only”, while RNA is a transcript that requires cutting and pasting before finalization. Often times, over half of the base pairs of precursor messenger RNA, or pre-mRNA, compose introns, or non-coding regions (Garcia-Blanco, 2004). In one of the most significant post-transcriptional modifications, these introns are removed by spliceosomes, leaving the exons that contain actual information used during translation. The splicing process involves many small nuclear RNA proteins that bind to the intron’s 3’ and 5’ ends and fold the segment into a loop that is cleaved off. However, in a phenomenon known as alternative splicing, which occurs in more than 60% of genes, some introns are treated as exons and vice versa, allowing the same sequence to encode distinct proteins (Edwalds, 2010).