Honorable Mention Excerpts
Naperville Central High School
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.
Eleanor Roosevelt High School
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.
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.
The John Cooper School
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.
Carrboro High School
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.,
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).
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).
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
…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).
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 .
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).