Re: [hgvs-nomenclature] Follow Up 1: Elsevier Permission Request < Francesc (Paco) Palau: Nelson Pediatric Textbook of Rare Diseases, 1, 9780443115110 > <DEL_Palau_1

https://hgvs-nomenclature.org/stable/background/refseq/#rna-reference-sequence-r

From: Fokkema, I.F.A.C. (HG) <I.F.A.C...@LUMC.nl>
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Subject: Re: [hgvs-nomenclature] Follow Up 1: Elsevier Permission Request < Francesc (Paco) Palau: Nelson Pediatric Textbook of Rare Diseases, 1, 9780443115110 > <DEL_Palau_1_chaithanyaa> Table 2.3 [250923-003223]

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Table 2-3_updated.docx

Fokkema, I.F.A.C. (HG)

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Oct 3, 2025, 11:56:34 AM10/3/25

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Dear Athulya,

Thank you for the updated table. Please note that the description for RNA reference sequences remains incorrect. The r. only starts counting at the first nucleotide for non-coding transcripts. For coding transcripts, the r. starts counting at the c.1. Please see:

"nucleotide numbering for an RNA reference sequencing follows that of the associated coding or non-coding DNA reference sequence; nucleotide r.123, relates to c.123 or n.123."

Best regards,

Ivo Fokkema

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Subject: RE: [hgvs-nomenclature] Follow Up 1: Elsevier Permission Request < Francesc (Paco) Palau: Nelson Pediatric Textbook of Rare Diseases, 1, 9780443115110 > <DEL_Palau_1_chaithanyaa> Table 2.3 [250923-003223]

Permissions Seeking

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Dear Ivo Fokkema,

Thank you for your email.

We will check with editorial and make necessary corrections.

Kind regards,

Thomas Rexson Yesudoss

Customer Relationship Specialist

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From: Ivo Fokkema
Date: Friday, October 03, 2025 03:57 PM GMT

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From: Thomas Rexson Yesudoss
Date: Monday, September 29, 2025 03:26 AM GMT

Dear Ivo Fokkema,

Thank you for keeping us informed.

We will check this internally with our editorials on this and confirm you shortly.

Kind regards,

Thomas Rexson Yesudoss

Customer Relationship Specialist

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From: Ivo Fokkema
Date: Tuesday, September 23, 2025 06:50 AM GMT

Dear Thomas,

In addition to Reece's comment, please note that the table you showed contains incorrect information. The link Reece referred to, contains the correct information. Please have the authors revise the table based on the updated information. For instance, the information on the RNA numbering is incorrect. The correct information is indicated on the page Reece linked to:

"nucleotide numbering for an RNA reference sequencing follows that of the associated coding or non-coding DNA reference sequence; nucleotide r.123, relates to c.123 or n.123."

Also, LRG reference sequences are no longer created, and therefore, are no longer recommended.

Best regards,

Ivo Fokkema

From: Thomas Rexson Yesudoss
Date: Tuesday, September 23, 2025 06:10 AM GMT

[---002:008613:07877---]

Ajith, Athulya (ELS-CHN)

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Dec 18, 2025, 5:16:20 AM12/18/25

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Dear Ivo Fokkema,

We have now updated the table as per the suggestion. I have attached the updated table herewith the email for your reference. Could you please let me know if this is correct?

Thank you!

Best Regards,

Athulya

Athulya Ajith

Copyrights Specialist, Permission Team

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Subject: Re: [hgvs-nomenclature] Follow Up 1: Elsevier Permission Request < Francesc (Paco) Palau: Nelson Pediatric Textbook of Rare Diseases, 1, 9780443115110 > <DEL_Palau_1_chaithanyaa> Table 2.3 [250923-003223]

Dear Ivo Fokkema,

Thank you for your email.

We will check with editorial and make necessary corrections.

Kind regards,

Thomas Rexson Yesudoss

Customer Relationship Specialist

ELSEVIER | HCM - Health Content Management

From: Ivo Fokkema

Date: Friday, October 03, 2025 03:57 PM GMT

/span>

From: Thomas Rexson Yesudoss
Date: Monday, September 29, 2025 03:26 AM GMT

Dear Ivo Fokkema,

Thank you for keeping us informed.

We will check this internally with our editorials on this and confirm you shortly.

Kind regards,

Thomas Rexson Yesudoss

Customer Relationship Specialist

ELSEVIER | HCM - Health Content Management

From: post master

Date: Saturday, September 27, 2025 06:13 AM GMT

Hello, this is the mail server on mailgwln05.rightnowtech.com.

I am sending you this message to inform you on the delivery status of a
message you previously sent. Immediately below you will find a list of
the affected recipients; also attached is a Delivery Status Notification
(DSN) report in standard format, as well as the headers of the original
message.

<enqu...@hgvs.org> delivery failed; will not continue trying

Unsupported message type - delivery-status, message attachment discarded.

From: Ivo Fokkema
Date: Tuesday, September 23, 2025 06:50 AM GMT

Dear Thomas,

In addition to Reece's comment, please note that the table you showed contains incorrect information. The link Reece referred to, contains the correct information. Please have the authors revise the table based on the updated information. For instance, the information on the RNA numbering is incorrect. The correct information is indicated on the page Reece linked to:

"nucleotide numbering for an RNA reference sequencing follows that of the associated coding or non-coding DNA reference sequence; nucleotide r.123, relates to c.123 or n.123."

Also, LRG reference sequences are no longer created, and therefore, are no longer recommended.

Best regards,

Ivo Fokkema

[---002:008613:07877---]

Table 2-3_updated.docx

Permissions Seeking (ELS)

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Dec 30, 2025, 8:57:43 AM12/30/25

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Hi Reece,

Hope you will find this email well.

I would like to follow up with you on the below email. We have made the suggested updates to the table. Could you please let me know if this is correct?

Looking forward to hearing from you. Thanks in advance!

Best Regards,

Athulya

Athulya Ajith

Copyrights Specialist, Permission Team

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Table 2-3_updated.docx

Reece Hart

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Dec 30, 2025, 6:37:38 PM12/30/25

to Permissions Seeking (ELS), Ivo Fokkema, HGVS Nomenclature

That looks generally right to me.

Note the double opening parentheses.

I recommend remaining the third column as "Numbering System" and in each cell define the range of numbering. For example, for genomic sequence, numbering is 1 through the length of the sequence. The problem with the current presentation is that "1" not explicitly stated as the first position. Some numbering systems would state that the first position is "0".

Permissions Seeking (ELS)

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Jan 12, 2026, 4:00:57 AM (8 days ago) Jan 12

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Dear Reece,

Hope you will find this email well.

I have attached the updated Table herewith the email as per the suggestions.

Could you please review this and let me know if we have the permission to use the content.

Looking forward to hearing from you. Many thanks in advance.

Best Regards,

Athulya

Athulya Ajith

Copyrights Specialist, Permission Team

ELSEVIER | HCM Publishing Services

From: Permissions Seeking <Permissi...@elsevier.com>

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Subject: Re: [hgvs-nomenclature] Follow Up 1: Elsevier Permission Request < Francesc (Paco) Palau: Nelson Pediatric Textbook of Rare Diseases, 1, 9780443115110 > <DEL_Palau_1_chaithanyaa> Table 2.3 [250923-003223] [251231-005870]

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For queries on permission processes, please refer to FAQ. For guidance on applying for permissions and filling the permission log, please refer here

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From: Reece Hart
Date: Tuesday, December 30, 2025 11:37 PM GMT

That looks generally right to me.

Note the double opening parentheses.

I recommend remaining the third column as "Numbering System" and in each cell define the range of numbering. For example, for genomic sequence, numbering is 1 through the length of the sequence. The problem with the current presentation is that "1" not explicitly stated as the first position. Some numbering systems would state that the first position is "0".

Hi Reece,

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Table 2-3_updated_revised.docx

Permissions Seeking (ELS)

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Jan 14, 2026, 8:28:57 AM (6 days ago) Jan 14

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URGENT:

Dear Team,

I hope you're doing well.

I’m following up once again regarding our permission request for the use of a figure copyrighted to you.

As we are nearing our final permissions deadline, your prompt response would be greatly appreciated. If permission can be granted, kindly confirm via email.

Please refer to the email thread below for full request details. Do let me know if any further information is needed.

Thank you again for your time and support.

Best Regards,

Athulya

Athulya Ajith

Copyrights Specialist, Permission Team

ELSEVIER | HCM Publishing Services