Technical Details

This is the first in a series of technical posts I hope to put together over the coming weeks about the process of creating Stranger Visions. Starting from the lab end I will describe in detail how I create these portraits from DNA.

The first step of course is extracting DNA from a sample, that can be done with a kit readily obtainable from Qiagen, the “DNA Investigator Kit”.

After I extract the DNA* I do a test PCR for a specific alu insertion using a primer (full kit is also available) from Carolina. This gives me an idea of whether I successfully extracted chromosomal DNA or not. If the results look bad on this there is probably no reason to go further with this sample.

Next is looking at maternal ancestry from mitochondrial DNA. A couple different primer/kits are also available from carolina to look at this region amplifying for sequencing and  haplotyping.

If all these results look good I continue to look at 3 SNPs associated with particular traits and 1 region on the y chromsome:

rs12913832 – for eye color

SRY gene – present on Y chromosome, I use to indicate gender

rs9939609 – as one of many indicators of obesity

rs4648379 – preliminary research, correlated with the size of the nose

I have been using a free tool on IDT for designing primers to target these regions using PCR. If the result of the reactions looks good in a gel I send them for sequencing.
So those are SNPs I have had success so far analyzing in the lab myself, but there are a whole lot more clues I have on a “master list”, the things I can find out from a 23andme profile for example. In addition to SNPs related to specific traits this includes Y chromosome haplogroup information from males to get an idea of paternal ancestry, as well as Ancestry Informative Markers, specific SNPs that are correlated with population studies giving an overall picture of ancestry beyond the direct maternal and paternal lineage. I am pasting my master list here below (excluding the ancestry info I just mentioned and linked to above as that would increase the list a thousand fold). Also, here is a link to appearance related SNPs on snpedia.

*I have recently discovered that whole genome amplification can also be performed after the extraction step and isn’t as expensive as I previously though – I will likely pursue this in future experiments.

SNPalleleassociated trait
rs642742AAwest african
rs1426654AAlight skinned european
rs2814778CCmalaria resistance
rs17646946 GGcurlier hair in europeans
rs11803731AAstraighter hair
rs12896399TTblue eyes vs green if not brown – prelim research
rs1426654AAeuro ancestry – light skinned
rs12913832GGblue eyes
rs1667394CCdecreased odds blond hair
rs1805007TThigher odds red hair
rs17822931 TTdry earwax
rs1851665AAgreater chance of obesity
rs2153271TTmore freckling
rs7349332CT;TTcurlier hair
rs6732426CCcurlier hair
rs3827760 AGthinner hair (asian)
rs9939609AAhigher BMI
ATtypical BMI
TTlower BMI
rs6548238  CCtypical BMI
CT;TTlower BMI
rs925946 GTtypical BMI
TThigher BMI
GGlower BMI
rs7138803  AGtypical BMI
AAhigher BMI
GGlower BMI
rs13130484 CTtypical BMI
TThigher BMI
CClower BMI
rs4788102 AGtypical BMI
AAhigher BMI
GGlower BMI
rs10838738AGtypical BMI
GGhigher BMI
AAlower BMI
rs10871777 GG;AGhigher BMI
rs1393350AAblue eyes rather than green IF non-brown – preliminary research
rs1533995AAmore pronounced crypts
GGless pronounced crypts
AC,CCless iris furrows
rs12896399GGmore pronounced pigementation rings
TTabsent pigmentation rings
CTslightly higher odds red hair
rs1805009CCred hair
TTincreased odds brown hair
CCless freckling
rs4778138GGless freckling
AAmore freckling
rs1805007CT;TTmore freckling
rs1042602AAabsence of freckles
rs2733832CCdarker skin
CT;TT lighter skin
rs1800414Ceach c -> 1.3 melanin unit lighter skin in east asians
rs16891982GGeuropean light skinned
preliminary facial researchsource
rs4648379C/Tedge of nostril -> tip of lower nose
rs974448C/Tmid eye to top of nose
rs17447439A/Gdistance between eyes
rs6555969C/Tdistance between cheekbone and nose, ALSO distance between eye and top nose
rs805722C/Tdistance between eye and top of nose
Eye and Skin colorsource
find the cost of your paper

Shuffle An Array

Today’s exercise comes to us from Leetcode via Reddit:

Given an array consisting of 2n elements in the form
[x1,x2,…,xn,y1,y2,…,yn], return the array in the form [x1,y1,x2,y2,…,xn,yn].

The Reddit poster claims to be new to Scheme and functional programming, and was thinking of a solution using length and list-ref, but couldn’t solve the problem.

Your task is to show the student how to solve the problem. When you are
finished, you are welcome to read or run a suggested solution, or to post your own solution or discuss the exercise in the comments below.

Blog Tour Review: Haunting the Deep by Adriana Mather

Haunting the Deep (How to Hang a Witch, #2) by Adriana Mather

Publisher: Knopf Books for Young Readers
Series: How to Hang a Witch, #2
Publication date: 10/03/2017
Source: Publisher

The Titanic meets the delicious horror of Ransom Riggs and the sass of Mean Girls in this follow-up to the #1 New York Times bestseller How to Hang a Witch, in which a contemporary teen finds herself a passenger on the famous “ship of dreams”—a story made all the more fascinating because the author’s own relatives survived the doomed voyage.

Samantha Mather knew her family’s connection to the infamous Salem Witch Trials might pose obstacles to an active social life. But having survived one curse, she never thought she’d find herself at the center of a new one. 

This time, Sam is having recurring dreams about the Titanic . . . where she’s been walking the deck with first-class passengers, like her aunt and uncle. Meanwhile, in Sam’s waking life, strange missives from the Titanic have been finding their way to her, along with haunting visions of people who went down with the ship. 

Ultimately, Sam and the Descendants, along with some help from heartthrob Elijah, must unravel who is behind the spell that is drawing her ever further into the dream ship . . . and closer to sharing the same grim fate as its ghostly passengers.

Haunting the Deep is the follow up to How to Hang a Witch which follows Sam on another ghostly mission to break a spell that could quite possibly send Sam to watery grave. Anything and everything Titanic related intrigues me and the fact that this book follows Sam as she tries to navigate the mysterious workings that kept luring her onto the Titanic was just as spellbinding. Mather continues to impress by magically weaving a fascinating tale which was inspired by her own relatives surviving the voyage.

This book kept me immersed in its wonderfully woven mystery and never let go. I couldn’t put this book down no matter how many times I knew I needed to get some sleep before work. I couldn’t be more satisfied with how everything unfolded in this book. It was so great to live and experience with these characters. Fans of How to Hang a Witch will be thrilled that this book is just as captivating.

Haunting the Deep is a great follow up to How to Hang a Witch. The history, the magic, and yes the ghosts are just as enchanting. I would recommend this book to readers of all ages! It’s just that impressive!

Rating: 4.5 out of 5 Stars

Check out the book trailer!

Traveling West Virginia – Hawks Nest – New River Gorge Trail

We don’t do as much traveling as we used to. But we recently took a day trip to southern West Virginia.

Our first stop was Hawks Nest State Park. If you have traveled there before, you know where they get the expression half the fun is getting there – that is unless you are prone to motion sickness. If you are, then I would advise you to sit in the front seat of the car.

We have been to Hawks Nest many times, but this is the first time we ever rode the tram down to the river.

We wanted to ride the jet boats, but they were all booked up.

 So we did the next item on our list. We went on a hike. My husband has a bad knee, so he didn’t go with my son and me. He loves to talk, so he stayed and talked to the tram guys.

The hike was beautiful – a path filled with large rocks, rhododendron, foot bridges, caves, snakes . . .

Of course, my son had to climb up onto the first big rock we came to. Boys will be boys.

And speaking of snakes. This is where I encountered a baby snake wriggling under my shoe. I didn’t stay long enough to see what kind he was, but he wasn’t a black snake.

On the way back down the trail on this neat little foot bridge.

Our next stop was at a trail we had never walked on before. You drive over the New River Gorge Bridge, which is an experience I never tire of, and then travel a local road to a set of trails that take you to a great place for a photo op of the bridge.

I never took any pictures along the trail because we were in a hurry. We even sprinted in a few places. I never walked a trail so fast in my life. It was late and given the length of the trail we were going to be walking back in the dark. Thank goodness for cell phone flash lights!

The first mile and 3/4 was a fairly easy walk. But the last 1/4 mile was a heavy breather. This is approaching the end of the trail. And believe me when I tell you the view was well worth the huffing and puffing. 

This was as far out as I would venture. My son said that I couldn’t fall off unless I just walked off the edge. I said different — You could trip. You could slide. You could get woozy. So I played it safe.

We still got some great pictures. My son even took a few selfies.

After enjoying the view and taking a bunch of pictures, we started back. And yes, it was in the dark. I kept imagining encounters with wild animals, but none appeared.

My son said, “If we see Big Foot, shine the light while I take the picture.”
I told him, “Please make it a clear picture.”
For some reason all the pics people take of Big Foot are blurry. 😊

Press this link to a list of trails in the area. I would like to try them all out. The name of the trail we took is the Long Point Trail.

 Hope you enjoyed this Traveling West Virginia.

Have you ever been to either of these places?

If not, I hope you get to visit some day.