Wednesday, March 20, 2019

GRCh38.p13 has been released


The GRC is pleased to announce that GRCh38.p13 is now available! This release adds 45 new scaffolds: 43 FIX patches and 2 NOVEL patches. The FIX patch scaffolds provide assembly corrections while the NOVEL patch scaffolds deliver new alternate sequence representations. A valuable contribution to this patch release comes in the addition of the Nucleolus Organiser Region (NOR) sequences for the short arms of the acrocentric chromosomes (13, 14, 15, 21, and 22) as provided by Brian McStay's group (PMID: 23990606). The NOR additions will be discussed in detail in a separate blog.

With access to an ever-increasing pool of high quality, long-read human assembly data, the GRC has been able to utilise this in GRCh38.p13 to address genome issues that have until now persisted due either to lack of data, or complexity. Much of the data added in this patch is derived from the CHM1 human haploid hydatidiform mole assembly (GCA_001297185.2). Originally produced as part of an assembly comparison analysis (see PMID: 
28396521), the assembly was recently Pilon corrected and re-submitted to GenBank by the McDonnell Genome Institute at the Washington University, a GRC center, with the specific aim of improving the base pair accuracy for use of its sequences in improving the Human Genome Reference.

In GRCh38.p13, a total of 28 assembly gaps have been closed. These updates, together with sequences added to correct 5 clone errors, add more than 0.5 Mb of unique data to the assembly. The majority of unique sequences added in this release come from contigs that are components of WGS assemblies derived from PacBio sequence reads, such as the CHM1 assembly mentioned above. However, genomic clone libraries still play an important role in assembly curation. In this release BAC clones from human cell line (CHM1htert) have provided complete, single haplotype representations of clinically important regions such as Prader-Willi on chromosome 15, and CT47 on chromosome X.

The CT47 cancer/testis antigen located on human Xq24 is organized as an array of 4.8 kb tandemly repeated units. Due to the repetitive nature of the sequence involved, coupled with the limitations of the technologies available at the time, the representation of the CT47 gene cluster in GRCh37 and GRCh38 was problematic. The region is gapped, and the flanking clones are from different haplotypes. As a consequence, the representation of the cluster in these assemblies was incomplete and biologically unsound, representing an indeterminate number of gene copies (Figure 1, top).
Studies have indicated that this polymorphic array is highly variable between haplotypes and ranges from 4 to 17 copies in length. Long-read sequencing of genomic clones has now captured the complete CT47 cluster as a single haplotype. The fix patch (ML143381.1) included in the GRCh38.p13 release now provides a contiguous and validated representation of the CT47 genomic region. This patch closes the assembly gap with sequences from BAC clone AC275592.1 (CH17-182I12) which contains a complete, 7 copy representation of the CT47 array (Figure 1, bottom). Note that this update reduces the number of CT47 genes represented as compared to GRCh37 and GRCh38.
Figure 1 Top: CT47 region in GRCh38. Incomplete representation of CT47 gene cluster in GRCh38 due to an assembly gap. Bottom: CT47 fix patch in GRCh38.p13. The gap is closed and a complete representation of CT47 cluster is provided. 
Optical mapping technology has been used to confirm the copy number for the CT47 array is accurate for the haploid CHM1tert sample (Figure 2), from which the clone library was derived.
Figure 2: AC275592.1 alignment to CHM1 Bionano optical map.

As more data becomes available using the latest technologies the GRC is able to utilise this in order to continually to update and improve the reference genome. If you have questions about this process, let us know.

You can download the GRCh38.p13 assembly, including the alignments of the patches to GRCh38, from the GenBank FTP.


22 comments:

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  7. I'm 40 years old female I tested genital herpes (HSV1-2) positive in 2002. I was having bad outbreaks. EXTREMELY PAINFUL. I have try different kinds of drugs and treatment by the medical doctors all to know was avail. Six months ago I was desperately online searching for a helpful remedies for genital herpes (HSV1-2) cure, which i come across some helpful remedies on how Dr OYAGU have help so many people in curing genital herpes (HSV1-2) with the help of herbal treatment because I too believe there is someone somewhere in the world who can cure herpes completely. At of the past 2 months, however, I've been following his herpes protocol Via oyaguherbalhome@gmail.com or +2348101755322 and it stopped all outbreaks completely! To my greatest surprise I was cured completely by following the protocol of his herbal medicine . Don't be discouraged by the medical doctors. There is a cure for HSV with the help of herbs and roots by a herbalist Dr call Dr OYAGU he is so kind and truthful with his herbal treatment, kindly contact him for more information Via oyaguherbalhome@gmail.com or WhatsApp DR on +2348101755322 or vist his website https://oyaguspellcaster.wixsite.com/oyaguherbalhome you will be lucky as i am today

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  8. God bless Dr. USELU for his marvelous work in my life, I was diagnosed of HERPES SIMPLEX VIRUS since 2018 and I was taking my medications, I wasn’t satisfied i needed to get the HERPES out of my system, I searched about some possible cure for HERPES i saw a comment about Dr. USELU , how he cured HERPES with his herbal medicine, I contacted him and he guided me. I asked for solutions, he started the remedy for my health, he sent me the medicine within 3 days. I took the medicine as prescribed by him and 2weeks later i was cured from HERPES contact him via email (dr.uselucaregiver@gmail.com) once again thanks to you Dr. USELU cure the flowing virus, contact his email or add him on whatsapp (+2347052898482) cancer cure
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  10. God bless Dr. USELU for his marvelous work in my life, I was diagnosed of HERPES SIMPLEX VIRUS since 2018 and I was taking my medications, I wasn’t satisfied i needed to get the HERPES out of my system, I searched about some possible cure for HERPES i saw a comment about Dr. USELU , how he cured HERPES with his herbal medicine, I contacted him and he guided me. I asked for solutions, he started the remedy for my health, he sent me the medicine within 3 days. I took the medicine as prescribed by him and 2weeks later i was cured from HERPES contact him via email (dr.uselucaregiver@gmail.com) once again thanks to you Dr. USELU cure the flowing virus, contact his email or add him on whatsapp (+2347052898482) cancer cure
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  11. DR OYAGU herbal medicine is a good remedy for herpes simplex virus cure. My name is MIGNON WRIGHT , am from USA,I am here to give my testimony about DR OYAGU who helped me in my life, i want to inform the public how i was cured from (HERPES SIMPLEX VIRUS) by DR OYAGU, i visited different hospital but they gave me list of drugs like Familiar, Zovirax, and Valtrex which is very expensive to treat the symptoms and never cured me. I was browsing through the Internet searching for remedy on HERPES and i saw comment of people talking about how DR OYAGU cured them, when i contacted him he gave me hope and send a Herbal medicine to me that i took and it seriously worked for me, am a free person now without any problem, my HERPES result came out negative, I pray to God to never let me and my family forget you in our life,am now cured permanently, you can also get your self cured my friends if you really need this doctor help, you can reach him now his website https://oyaguspellcaster.wixsite.com/oyaguherbalhome Email: oyaguherbalhome@gmail.com or via whatsapp +2348101755322

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  13. DR OYAGU herbal medicine is a good remedy for herpes simplex virus cure. My name is MIGNON WRIGHT , am from USA,I am here to give my testimony about DR OYAGU who helped me in my life, i want to inform the public how i was cured from (HERPES SIMPLEX VIRUS) by DR OYAGU, i visited different hospital but they gave me list of drugs like Familiar, Zovirax, and Valtrex which is very expensive to treat the symptoms and never cured me. I was browsing through the Internet searching for remedy on HERPES and i saw comment of people talking about how DR OYAGU cured them, when i contacted him he gave me hope and send a Herbal medicine to me that i took and it seriously worked for me, am a free person now without any problem, my HERPES result came out negative, I pray to God to never let me and my family forget you in our life,am now cured permanently, you can also get your self cured my friends if you really need this doctor help, you can reach him on his website https://oyaguspellcaster.wixsite.com/oyaguherbalhome Email: oyaguherbalhome@gmail.com or via whatsapp +2348101755322

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  14. I already gave up on ever getting cured of HSV2 because i have try many treatment none of them work out for me i have be to different hospital they always tell me same thing there is no cure for herpes when i came across a post about Dr oyagu, in the net from a lady called Rebecca i contacted him and he reassured me with his herbal medicine which i took according to the way he instructed, that how i was cured. I doubted at first because i have been to a whole lot of reputable doctors, tried a lot of medicines but none was able to cure me. so i decided to listen to him and he commenced treatment, and under two weeks i was totally free from Herpes. i want to say a very big thank you to DR oyagu for what he has done in my life. feel free to leave him a message on email oyaguherbalhome@gmail.com and also WhatsApp him +2348101755322.. or vist his website https://oyaguspellcaster.wixsite.com/oyaguherbalhome. He can still be able to help you with this herbs medicine: 1...ALS CURE/DIABETES CURE/EPILESY/HPV CURE/LUPUS/HEPATITIS/CANCER/GOUT

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  15. Herpes Virus is a very terrible virus, if not for my Husband and the help of the great Dr. OSE my life would have been a mess! I was diagnosed with Herpes virus in 2014, my husband encouraged me, and told me not to lose hope, I managed to give birth to a baby Boy who was free from this virus, and my Husband was always there for me! One day he came to me and told me that he had found a man who could cure me. Based on scientists, they said there is no cure for Herpes virus; he told me that he has seen many testimonies about him on the internet. We decided to contact him, we filled his Herbal home form, and he asked us to buy some local root and herbs items which we did! and he prepared for me a herbal medicine and 14 days later he asked me to go for a medical test, faithfully hopefully i went for the medical test, and Behold, I was cured from this virus and it was not found in my Body system again... My Dear Husband and my Father Dr. OSE, God will surely bless the both of you till the end of time, in Jesus name.. If you have any problem kindly contact via his Email: droseherbalhome@gmail.com..

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  16. It’s obvious some patients with herpes are being enslaved to the antiviral and other supplementary Orthodox medicine just to help suppress the virus and not a cure. I have been with the virus since 2015 until I was introduced by a blogger who also narrated her story online on how she was cured of Genital Herpes after using Dr Sikies Herbal Medicine. This is a year and 2 weeks since I was delivered from genital Herpes. All thanks to God for using this Great herbalist to heal me. I have promised to keep telling good things about Dr Sikies. Please feel free to share Your problems with him and don’t forget to tell him I did refer you to Him. Thanks. Write him on mail Drsikies@gmail.com He deals with Alzheimer virus, Cancer, HIV, Herpes, Genital, warts, ALS, BV, UTI, Virginal infection, Genital, Wart, HPV, Hepatitis A/B, Good luck, HSV, Pregnancy, Ex back.  

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    ReplyDelete
  17. Good news this is to everyone out there with different health challenges, as I know there are still a lot of people suffering from different health issues and are therefore looking for solutions. I bring you Good news. There is a man called Dr ehiaguna a herbal practitioner who helped cure me from HSV (2), i had suffered from this diseases for the past 5 years and i have spent so much money trying to survive from it. I got my healing by taking the herbal medicine Dr ehiaguna sent to me to drink for about 14 days . 3 days after completion of the dosage, I went for a medical checkup and I was tested free from HSV. all thanks to God for leading me to Dr ehiaguna who was able to cure me completely from this deadly diseases, I’m sharing this so that other people can know of this great healer called Dr ehiaguna because I got to know him through elizabeth who he cured from HIV. I was made to understand that he can cure several other deadly diseases and infections. Don’t die in ignorance or silent and don’t let that illness take your life. Contact Dr ehiaguna through his email  drehiaguna@gmail.com You can also whatsapp/call him on:+2348073908953 . Visit his website  https://effectiveherbalcurehome.blogspot.com/   He cure all forms of disease {1}HIV/AIDS {2}DIABETES {3}EPILEPSY {4} BLOOD CANCER {5} HPV {6} BRAIN TUMOR {7} HEPATITIS {8}COPD{9} SICKLE AND ANAEMIA.etc Be kind enough to share as you received.  

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  18. DON'T BELIEVE THERE IS A CURE FOR HERPES? Well here is my testimony about a doctor who helped me when I was infected with HERPES on September 22, 2014, I went to many hospitals for cure but there was no solution, so I was thinking how can I get a solution so that my body can be okay. One day I was online and i saw the testimony of Mrs Amy Kendral speaking on how a man called Dr Razor helped her Eradicate the Herpes Simplex Infection that was eating her up every day, I Immediately emailed the Herbal Doctor Razor with the Details provided by This Woman on how to reach Him and I explained everything to him. Dr Razor told me all the things I needed to do and also gave me instructions to take a wish I followed properly. Before I knew what was happening after 18 days of taking the medication I started having changes in my body, so i told the herbalist of the development in my health and he asked me to go for a medical check up, the Doctors There were Amazed that Herpes have a Permanent and complete cured. Doctor Razor's website :  https://herbalistrazorherb.wixsite.com/drrazorherbalhome. You can Reach him on his Email via drrazorherbalhome@gmail.com . WhatsApp/Call him on +2349065420442. I made sure the Virus wasn't laying dormant in my nerve cells because I have heard of a situation like that. Before deciding to write this testimony so that many who are Battling with different kinds of Challenges Can also get cured.

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